This document is mainly for part5 of the GEO data set analysis, that is the normalisation and batch correction step.
Cord blood only have one sample.
library(tidyverse)
library(readxl)
library(minfi)
library(magrittr)
library(tibble)
library(data.table)
library(limma)
library(ewastools)
library(ENmix)
library(wateRmelon)
library(FactoMineR)
library(WGCNA)
library(impute)
library(ChAMP)
library(sva)
library(quantro)
library(doParallel)
library(ggplot2)
library(RColorBrewer)
pal <- brewer.pal(8, "Dark2")
# GEOmeta, GEO_phenotypes
load(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/GEO_phenotypes_add10.RData")
# Msets
# Mset_450k_normalPlacenta_v1, Mset_EPIC_normalPlacenta, Mset_EPIC_normalPlacenta_ourStudy,
# Mset_450k_Amnion, Mset_EPIC_Amnion, # Mset_450k_Chorion, Mset_EPIC_Chorion,
# Mset_450k_Decidua, Mset_EPIC_Decidua, # Mset_450k_MaternalBlood_v1, Mset_450k_mesenchyme,
# Mset_450k_trophoblast, Mset_450k_UC, Mset_450k_UCB,
load(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/MsetsOf9TissueTypes.RData")
# Join.df_v2, GEO_phenotypes_joinedSamples, MDS_joinedSamples
load(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/GEO_joinedSamples551_Beta_MDS.RData")
# annotation needed for using functions
ann450k <- readRDS(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/ann450k_GEO15sets.rds")
annEPIC <- readRDS(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/annEPIC_GEO15sets.rds")
There are many tissue types for normal tissue samples around placenta, such as cord blood, chorionic plate and so on. I used modified BMIQ method to normalise different tissue separately.
** When I used GSE74738 as gold standard, the batches were not corrected very well; Then I try to use GSE75248 as gold standard because this dataset have 174 placental samples which is the biggest dataset for placenta sampels. However, the result of this calibration is even worse than using GSE74738 as gold standard**
There are 9 tissue types (we choose tissue types located near placenta) in total from GEO.
NormFUN,BMIQcalibration function will be used in the NormFUN chunk.# `BMIQcalibration` function in `BMIQ_Horvath.R`
source(file = "~/DNAme/Process_decidual/Rcodes/BMIQ_Horvath.R")
## Loading required package: RPMM
## Loading required package: cluster
##
## Attaching package: 'RPMM'
## The following object is masked from 'package:limma':
##
## ebayes
CalibrateFUNWe first need to normalise with BMIQ and then calibrate data with BMIQ_calibration use my CalibrateFUN
# annotation: ann450k or annEPIC, need to be a DataFrame, annataion from the illumina annotation package
registerDoParallel(cores = 10)
# do BMIQ normalisation for all Msets
Msets <- c('Mset_450k_normalPlacenta_v1', 'Mset_EPIC_normalPlacenta', 'Mset_EPIC_normalPlacenta_ourStudy',
'Mset_450k_Amnion', 'Mset_EPIC_Amnion',
'Mset_450k_Chorion', 'Mset_EPIC_Chorion','Mset_450k_Decidua', 'Mset_EPIC_Decidua',
'Mset_450k_MaternalBlood_v1', 'Mset_450k_mesenchyme','Mset_450k_trophoblast',
'Mset_450k_UC', 'Mset_450k_UCB')
## normalise beta value for this tissue type
ListToJoin <- list()
# get BMIQ normalised beta values
for(i in Msets){
# get the object
Mset <- get(i)
# names for the list
listElements <- paste0("normB", str_replace_all(i, "Mset", ""), ".df")
# fill the list with beta values
ListToJoin[[listElements]] <- wateRmelon::BMIQ(beta.v = Mset) %>%
as.data.frame() %>% rownames_to_column(var="Probe")
}
## Loading required package: IlluminaHumanMethylation450kmanifest
# left_join values form all samples
Join_allNorm.df <- ListToJoin %>% purrr::reduce(left_join, by = "Probe")
# omit na values
Join_allNorm.df_v1 <- na.omit(Join_allNorm.df)
# as matrix
Join_allNorm.df_v2 <- Join_allNorm.df_v1 %>% remove_rownames() %>%
column_to_rownames(var="Probe") %>% as.matrix() # 298179
# phenotypes of all samples form all the tissue types
phenotype_matched <- GEO_phenotypes[match(colnames(Join_allNorm.df_v2),GEO_phenotypes$Sample_name),]
# M values
Mnorm <- log2(Join_allNorm.df_v2/(1 - Join_allNorm.df_v2))
Mnorm_v1 <- Mnorm[apply(Mnorm, 1, function(x) all(is.finite(x))), , drop=FALSE]
# plot MDS
## MDS for M values
MDS_norm551.M <- plotMDS(Mnorm_v1, top = nrow(Mnorm_v1),
labels = phenotype_matched$Sample, gene.selection = "common")
## MDS for Beta values
MDS_norm551.Beta <- plotMDS(Join_allNorm.df_v2, top = nrow(Join_allNorm.df_v2),
labels = phenotype_matched$Sample, gene.selection = "common")
# put into a list
NormBMlist <- list(NormBAll=Join_allNorm.df_v2, NormMAll=Mnorm_v1,
phenoDataAll=phenotype_matched,
MDS_norm551.Beta=MDS_norm551.Beta, MDS_norm551.M=MDS_norm551.M)
saveRDS(NormBMlist, file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/NormBMlist.rds")
CalibrateFUN calibrate all tissue types together, while CalibrateFUN2 calibrate data from different tissue types separately.TissueType could be: Placenta, Amnion, Chorion, Decidua, Maternal whole blood, placental mesenchyme, placental trophoblast, umbilical cord, Umbilical cord blood.
# write the BMIQ_calibration function: `CalibrateFUN` calibrate all tissue types together
CalibrateFUN <- function(GoldStaStudy){
# load data
NormBMlist <- readRDS(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/NormBMlist.rds")
## subset beta values for gold standard
GoldSta <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Study%in%GoldStaStudy,]
BetaMat_GoldSta <- NormBMlist$NormBAll[,colnames(NormBMlist$NormBAll)%in%GoldSta$Sample_name, drop=FALSE]
# calculate gold standard mean
BetaMat_GoldSta_t <- BetaMat_GoldSta %>% t()
gold.mean=as.numeric(apply(BetaMat_GoldSta_t,2,mean,na.rm=TRUE))
# use `BMIQcalibration` to normalise data; for inputs, rows are samples, colums are CpGs.
BetaMat_Calibrated <- BMIQcalibration(datM=t(NormBMlist$NormBAll), goldstandard.beta=gold.mean)
BetaMat_Calibrated_t <- BetaMat_Calibrated %>% t()
# match phenodata
BetaMat_Calibrated_phenoData <- NormBMlist$phenoDataAll[
match(colnames(BetaMat_Calibrated_t), NormBMlist$phenoDataAll$Sample_name),]
# return list containing beta and M values
## calculate M values
MMat_Calibrated <- log2(BetaMat_Calibrated_t/(1 - BetaMat_Calibrated_t))
MMat_Calibrated_v1 <-
MMat_Calibrated[apply(MMat_Calibrated, 1, function(x) all(is.finite(x))), , drop=FALSE]
# return beta and M values
BM_List <- list(Beta = BetaMat_Calibrated_t,
BetaPhenoData = BetaMat_Calibrated_phenoData,
M = MMat_Calibrated_v1)
return(BM_List)
}
# if I want to calibrate different tissue types seperately, I can use the following function
# CalibrateFUN2 <- function(GoldStaStudy){
# registerDoParallel(cores = 10)
#
# # load data
# NormBMlist <- readRDS(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/NormBMlist.rds")
#
# # all 9 tissue types
# # We removed "Maternal whole blood", because all maternal blood samples are from GSE66210, not the GSE74738
# TissueTypes <- c("Placenta", "Amnion", "Chorion", "Decidua",
# "placental mesenchyme",
# "placental trophoblast", "umbilical cord", "Umbilical cord blood")
#
# # create a list to hold all calibrated B values
# ListToJoin <- list()
#
# for(i in TissueTypes){
# # subset pheno data for each tissue type
# sampleNamesForOneTissue <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Sample%in%i,,drop=FALSE]
#
# BetaMat_1Tissue <- NormBMlist$NormBAll[,colnames(NormBMlist$NormBAll)%in%sampleNamesForOneTissue$Sample_name, drop=FALSE]
#
# ## subset beta values for gold standard
# GoldStaForOneTissue <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Sample%in%i &
# NormBMlist$phenoDataAll$Study%in%GoldStaStudy,,drop=FALSE]
#
# BetaMat_1Tissue_GoldSta <- NormBMlist$NormBAll[,colnames(NormBMlist$NormBAll)%in%GoldStaForOneTissue$Sample_name,
# drop=FALSE]
#
# # calculate gold standard mean
# BetaMat_1Tissue_GoldSta_t <- BetaMat_1Tissue_GoldSta %>% t()
# gold.mean=as.numeric(apply(BetaMat_1Tissue_GoldSta_t,2,mean,na.rm=TRUE))
#
# # use `BMIQcalibration` to normalise data; for inputs, rows are samples, colums are CpGs.
# BetaMat_1TissueCalibrated <- BMIQcalibration(datM=t(BetaMat_1Tissue), goldstandard.beta=gold.mean)
# BetaMat_1TissueCalibrated_t <- BetaMat_1TissueCalibrated %>% t()
#
# # names for the list
# listElements <- paste0("normCaliB_", str_replace_all(i, " ", "_"), ".df")
#
# # fill the list with beta values (9 tissue types)
# ListToJoin[[listElements]] <- BetaMat_1TissueCalibrated_t %>%
# as.data.frame() %>% rownames_to_column(var="Probe")
# } # end for
#
# # left_join values, to join all samples
# Join_allNormCali.df <- ListToJoin %>% purrr::reduce(left_join, by = "Probe")
#
# # omit na values
# Join_allNormCali.df_v1 <- na.omit(Join_allNormCali.df)
#
# # as matrix
# Join_allNormCali.df_v2 <- Join_allNormCali.df_v1 %>% remove_rownames() %>%
# column_to_rownames(var="Probe") %>% as.matrix() # 298179
#
# # phenotypes of all samples form all the tissue types
# AllNormCali_phenotype_matched <-
# NormBMlist$phenoDataAll[match(colnames(Join_allNormCali.df_v2),NormBMlist$phenoDataAll$Sample_name),]
#
# # M values
# MnormCali <- log2(Join_allNormCali.df_v2/(1 - Join_allNormCali.df_v2))
# MnormCali_v1 <- MnormCali[apply(MnormCali, 1, function(x) all(is.finite(x))), ,drop=FALSE]
#
# # return beta and M values
# BM_List <- list(Beta = Join_allNormCali.df_v2,
# BetaPhenoData = AllNormCali_phenotype_matched,
# M = MnormCali_v1)
# return(BM_List)
#
# }
CalibrateFUN to get normalised beta and M values for all the samples from 9 kinds of tissues located around placenta during early development.#, warning=FALSE, message=FALSE
# calibrate all data together, gold standard is GSE75248, the biggest study
normCali_BMof9TissueTypes_CaliTogether <- CalibrateFUN(GoldStaStudy = "GSE75248")
## [1] "Fitting EM beta mixture to goldstandard probes"
## [1] Inf
## [1] 0.004291609
## [1] 0.005029633
## [1] 0.005846578
## [1] 0.006186197
## [1] "Done"
## ii= 1
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005067143
## [1] 0.001306636
## [1] 0.001215709
## [1] 0.001026226
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 2
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003877849
## [1] 0.001418894
## [1] 0.001579609
## [1] 0.001723314
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 3
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004365881
## [1] 0.001252969
## [1] 0.001172409
## [1] 0.001116924
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 4
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003161242
## [1] 0.001462195
## [1] 0.002029076
## [1] 0.002012765
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 5
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003894542
## [1] 0.002908811
## [1] 0.003555411
## [1] 0.003471099
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 6
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003083511
## [1] 0.001712612
## [1] 0.002321906
## [1] 0.001997988
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 7
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003459549
## [1] 0.001538716
## [1] 0.001403033
## [1] 0.001497435
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 8
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004694951
## [1] 0.001179772
## [1] 0.001207254
## [1] 0.001167026
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 9
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003730109
## [1] 0.001460327
## [1] 0.001315005
## [1] 0.001431887
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 10
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003407794
## [1] 0.001394852
## [1] 0.002053395
## [1] 0.001939298
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 11
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00360314
## [1] 0.001340601
## [1] 0.001729715
## [1] 0.001995557
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 12
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003581482
## [1] 0.001947737
## [1] 0.002739098
## [1] 0.002717128
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 13
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003794867
## [1] 0.001569977
## [1] 0.002053563
## [1] 0.002150625
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 14
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004496709
## [1] 0.001981816
## [1] 0.003135482
## [1] 0.003312448
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 15
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004922474
## [1] 0.000970241
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 16
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004472581
## [1] 0.001709068
## [1] 0.001629776
## [1] 0.00196815
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 17
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005081555
## [1] 0.001427472
## [1] 0.0009279716
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 18
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003734995
## [1] 0.001021171
## [1] 0.001533956
## [1] 0.00176927
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 19
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003533846
## [1] 0.001055902
## [1] 0.001316381
## [1] 0.00153567
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 20
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00374296
## [1] 0.0009840665
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 21
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004312181
## [1] 0.001461938
## [1] 0.002213167
## [1] 0.002385601
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 22
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003697853
## [1] 0.001103485
## [1] 0.001195817
## [1] 0.001517793
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 23
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004162116
## [1] 0.001510772
## [1] 0.001400676
## [1] 0.001775739
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 24
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004128617
## [1] 0.00128873
## [1] 0.001450044
## [1] 0.001901674
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 25
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004522071
## [1] 0.001528997
## [1] 0.002519275
## [1] 0.002802847
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 26
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003930275
## [1] 0.001847127
## [1] 0.002622717
## [1] 0.002666898
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 27
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003597418
## [1] 0.001203049
## [1] 0.001765684
## [1] 0.002058149
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 28
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00338723
## [1] 0.001184752
## [1] 0.001182753
## [1] 0.001257635
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 29
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004171174
## [1] 0.002391013
## [1] 0.003266231
## [1] 0.003325166
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 30
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004373788
## [1] 0.001547527
## [1] 0.00110073
## [1] 0.001346364
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 31
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003459881
## [1] 0.00114724
## [1] 0.001797457
## [1] 0.001992013
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 32
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004041698
## [1] 0.001325446
## [1] 0.00143691
## [1] 0.001739361
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 33
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004020004
## [1] 0.001240853
## [1] 0.001335653
## [1] 0.001634525
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 34
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005104945
## [1] 0.001588248
## [1] 0.0008442185
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 35
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003746672
## [1] 0.001131619
## [1] 0.001461366
## [1] 0.001685703
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 36
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003209255
## [1] 0.001424919
## [1] 0.001759188
## [1] 0.001805924
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 37
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003361984
## [1] 0.00136832
## [1] 0.001493308
## [1] 0.001613815
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 38
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004088306
## [1] 0.001433486
## [1] 0.002470026
## [1] 0.002603205
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 39
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003343356
## [1] 0.001277959
## [1] 0.001490466
## [1] 0.0016537
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 40
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003401315
## [1] 0.001338783
## [1] 0.00133005
## [1] 0.001463034
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 41
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005846612
## [1] 0.001808963
## [1] 0.0009949937
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 42
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005124554
## [1] 0.001297124
## [1] 0.001073733
## [1] 0.001452885
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 43
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006927721
## [1] 0.002457688
## [1] 0.0007642155
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 44
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.008656618
## [1] 0.002839836
## [1] 0.0008041118
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 45
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007934933
## [1] 0.002563491
## [1] 0.0008628467
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 46
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006233611
## [1] 0.001391808
## [1] 0.0009873682
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 47
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.008162456
## [1] 0.002674148
## [1] 0.00118383
## [1] 0.0009234674
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 48
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005385914
## [1] 0.001815595
## [1] 0.001542165
## [1] 0.002367952
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 49
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007213605
## [1] 0.002145706
## [1] 0.0009097991
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 50
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005382652
## [1] 0.002237063
## [1] 0.00130486
## [1] 0.001850381
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 51
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006776544
## [1] 0.002083276
## [1] 0.0009757588
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 52
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004188348
## [1] 0.00100611
## [1] 0.001063449
## [1] 0.001345441
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 53
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006312141
## [1] 0.001821567
## [1] 0.0009925027
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 54
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007619912
## [1] 0.002714698
## [1] 0.000941782
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 55
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007583319
## [1] 0.002534264
## [1] 0.0009365599
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 56
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007293149
## [1] 0.002599594
## [1] 0.001427746
## [1] 0.0009260223
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 57
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004387704
## [1] 0.002063724
## [1] 0.003216016
## [1] 0.003476958
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 58
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004129308
## [1] 0.002255049
## [1] 0.00324841
## [1] 0.003468098
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 59
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00479807
## [1] 0.001903854
## [1] 0.002079449
## [1] 0.002536004
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 60
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004590951
## [1] 0.001768755
## [1] 0.002782744
## [1] 0.003091655
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 61
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004455463
## [1] 0.001665298
## [1] 0.002706028
## [1] 0.003013965
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 62
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00424136
## [1] 0.001475764
## [1] 0.002395649
## [1] 0.002966343
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 63
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004419531
## [1] 0.003032309
## [1] 0.003965154
## [1] 0.004143157
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 64
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004509253
## [1] 0.001966217
## [1] 0.00309514
## [1] 0.003389475
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 65
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003512167
## [1] 0.001368959
## [1] 0.001761701
## [1] 0.002141074
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 66
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003839689
## [1] 0.002614611
## [1] 0.003467823
## [1] 0.003679943
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 67
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004288229
## [1] 0.002029248
## [1] 0.003100741
## [1] 0.003390987
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 68
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004000395
## [1] 0.002487963
## [1] 0.003534424
## [1] 0.003813457
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 69
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004813793
## [1] 0.001871046
## [1] 0.002537869
## [1] 0.002922922
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 70
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0038456
## [1] 0.002443701
## [1] 0.003220766
## [1] 0.003347952
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 71
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00405508
## [1] 0.002965425
## [1] 0.003760021
## [1] 0.003929927
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 72
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004181849
## [1] 0.004276203
## [1] 0.004791003
## [1] 0.004912397
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 73
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003792661
## [1] 0.001770249
## [1] 0.002697929
## [1] 0.002799787
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 74
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003638617
## [1] 0.001411656
## [1] 0.001856491
## [1] 0.001963883
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 75
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00381878
## [1] 0.001297374
## [1] 0.001338194
## [1] 0.001695355
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 76
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004769504
## [1] 0.001204232
## [1] 0.001158578
## [1] 0.001196607
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 77
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004514159
## [1] 0.00147164
## [1] 0.001792244
## [1] 0.002240715
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 78
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003671755
## [1] 0.001415214
## [1] 0.002041457
## [1] 0.002232288
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 79
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003930275
## [1] 0.002269254
## [1] 0.003149868
## [1] 0.003309552
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 80
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004045339
## [1] 0.00151579
## [1] 0.002636788
## [1] 0.002743611
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 81
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004281317
## [1] 0.004505606
## [1] 0.00507722
## [1] 0.004578036
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 82
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004756495
## [1] 0.0058696
## [1] 0.006416131
## [1] 0.005741469
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 83
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004159017
## [1] 0.00286258
## [1] 0.003744762
## [1] 0.003740603
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 84
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004065614
## [1] 0.003903317
## [1] 0.00471985
## [1] 0.00464352
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 85
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003727498
## [1] 0.003913718
## [1] 0.004441187
## [1] 0.004022289
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 86
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004050544
## [1] 0.001463358
## [1] 0.00156857
## [1] 0.001789107
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 87
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003769487
## [1] 0.00148379
## [1] 0.002217537
## [1] 0.002396446
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 88
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003831118
## [1] 0.004598009
## [1] 0.005248864
## [1] 0.004772252
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 89
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003219121
## [1] 0.002901483
## [1] 0.003514718
## [1] 0.002954151
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 90
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00379106
## [1] 0.004455222
## [1] 0.004981593
## [1] 0.004438172
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 91
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00418034
## [1] 0.005630912
## [1] 0.006067683
## [1] 0.005582453
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 92
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002957797
## [1] 0.004269506
## [1] 0.004963253
## [1] 0.004624636
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 93
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004034679
## [1] 0.004347647
## [1] 0.00504792
## [1] 0.004672466
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 94
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003760309
## [1] 0.003371916
## [1] 0.003957653
## [1] 0.003618007
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 95
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004093396
## [1] 0.001337358
## [1] 0.001866704
## [1] 0.002274204
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 96
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003835873
## [1] 0.001404502
## [1] 0.002069992
## [1] 0.002400531
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 97
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00400928
## [1] 0.004339878
## [1] 0.004864835
## [1] 0.004333315
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 98
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004466197
## [1] 0.005348193
## [1] 0.005734195
## [1] 0.005075319
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 99
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004255194
## [1] 0.002127229
## [1] 0.003202328
## [1] 0.003334869
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 100
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004167863
## [1] 0.001927254
## [1] 0.00324796
## [1] 0.003452395
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 101
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003745884
## [1] 0.004759955
## [1] 0.005189724
## [1] 0.004724734
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 102
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004359085
## [1] 0.001616751
## [1] 0.002696252
## [1] 0.002892179
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 103
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003657104
## [1] 0.005519444
## [1] 0.006106155
## [1] 0.005368638
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 104
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003960427
## [1] 0.004286349
## [1] 0.004955176
## [1] 0.00454609
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 105
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003275481
## [1] 0.001676302
## [1] 0.001943591
## [1] 0.002032072
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 106
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0039857
## [1] 0.002128547
## [1] 0.003131069
## [1] 0.003050207
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 107
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002885545
## [1] 0.004765443
## [1] 0.004856769
## [1] 0.003841413
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 108
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003753185
## [1] 0.004160769
## [1] 0.004814346
## [1] 0.00487038
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 109
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004288331
## [1] 0.002784214
## [1] 0.003769208
## [1] 0.003922673
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 110
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00475723
## [1] 0.001905866
## [1] 0.003048717
## [1] 0.003386828
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 111
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003563071
## [1] 0.002154676
## [1] 0.00383207
## [1] 0.003768567
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 112
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00337089
## [1] 0.004197948
## [1] 0.00436183
## [1] 0.003499943
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 113
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003560965
## [1] 0.002560318
## [1] 0.003334692
## [1] 0.003323423
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 114
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003867995
## [1] 0.003805693
## [1] 0.004579179
## [1] 0.004296674
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 115
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00415579
## [1] 0.004312604
## [1] 0.004997468
## [1] 0.004602366
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 116
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004133218
## [1] 0.005113763
## [1] 0.005684807
## [1] 0.005432104
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 117
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005198075
## [1] 0.002106724
## [1] 0.002019559
## [1] 0.002589093
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 118
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003759695
## [1] 0.002497887
## [1] 0.003256023
## [1] 0.003139161
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 119
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004475687
## [1] 0.003292452
## [1] 0.004035347
## [1] 0.004025796
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 120
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004007585
## [1] 0.003225518
## [1] 0.004117764
## [1] 0.004312409
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 121
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003361211
## [1] 0.003065841
## [1] 0.003707044
## [1] 0.003192894
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 122
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004323934
## [1] 0.00150777
## [1] 0.002293318
## [1] 0.00259978
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 123
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004149653
## [1] 0.001418611
## [1] 0.002429501
## [1] 0.00273023
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 124
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003876026
## [1] 0.002590954
## [1] 0.003516852
## [1] 0.003683567
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 125
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003878655
## [1] 0.003438606
## [1] 0.004204967
## [1] 0.004133443
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 126
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004208991
## [1] 0.002375494
## [1] 0.003441819
## [1] 0.003706484
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 127
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004248078
## [1] 0.00255764
## [1] 0.003651103
## [1] 0.003815925
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 128
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00378125
## [1] 0.002218397
## [1] 0.003130613
## [1] 0.00320381
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 129
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00365763
## [1] 0.004671157
## [1] 0.004868855
## [1] 0.004042055
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 130
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004395697
## [1] 0.005135867
## [1] 0.005978977
## [1] 0.005779884
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 131
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003459261
## [1] 0.004606723
## [1] 0.004747691
## [1] 0.003932983
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 132
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004195673
## [1] 0.003272473
## [1] 0.004294337
## [1] 0.004318797
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 133
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003454597
## [1] 0.002960394
## [1] 0.003617382
## [1] 0.003221736
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 134
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003593236
## [1] 0.001716746
## [1] 0.002634587
## [1] 0.002742193
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 135
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004840486
## [1] 0.004059693
## [1] 0.004980444
## [1] 0.005049177
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 136
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00335156
## [1] 0.004665292
## [1] 0.004920574
## [1] 0.004054345
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 137
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003445738
## [1] 0.00459319
## [1] 0.005182513
## [1] 0.00446369
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 138
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004094796
## [1] 0.004125322
## [1] 0.00475285
## [1] 0.004450636
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 139
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004439598
## [1] 0.002934253
## [1] 0.004086884
## [1] 0.004114603
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 140
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003728544
## [1] 0.003139492
## [1] 0.004028566
## [1] 0.003813283
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 141
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003453877
## [1] 0.002164447
## [1] 0.003011743
## [1] 0.002862491
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 142
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003230132
## [1] 0.004072755
## [1] 0.004605569
## [1] 0.00406357
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 143
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004159414
## [1] 0.005327828
## [1] 0.005856989
## [1] 0.005617662
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 144
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00390249
## [1] 0.001441783
## [1] 0.001625086
## [1] 0.001596507
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 145
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003481659
## [1] 0.003928415
## [1] 0.004235317
## [1] 0.003529277
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 146
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004164987
## [1] 0.001447695
## [1] 0.00248598
## [1] 0.002795758
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 147
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003346307
## [1] 0.00191452
## [1] 0.002785611
## [1] 0.00281049
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 148
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003228306
## [1] 0.002437255
## [1] 0.003276694
## [1] 0.003139861
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 149
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004236131
## [1] 0.001631973
## [1] 0.002803267
## [1] 0.00312541
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 150
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003825526
## [1] 0.002396483
## [1] 0.003364374
## [1] 0.00343762
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 151
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003682787
## [1] 0.001422508
## [1] 0.002336723
## [1] 0.002611721
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 152
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004704799
## [1] 0.004871887
## [1] 0.005531211
## [1] 0.005461198
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 153
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004818054
## [1] 0.001570306
## [1] 0.001121144
## [1] 0.001624318
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 154
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004608978
## [1] 0.003001909
## [1] 0.003996895
## [1] 0.004128666
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 155
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003994001
## [1] 0.001984916
## [1] 0.004974334
## [1] 0.004842575
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 156
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0036025
## [1] 0.002004769
## [1] 0.002944389
## [1] 0.002959333
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 157
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003837578
## [1] 0.002317973
## [1] 0.003226816
## [1] 0.003307883
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 158
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003762386
## [1] 0.002116808
## [1] 0.00325169
## [1] 0.003539518
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 159
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003719249
## [1] 0.002453785
## [1] 0.003566767
## [1] 0.003642892
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 160
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00338387
## [1] 0.002115769
## [1] 0.00299003
## [1] 0.002952739
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 161
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003774645
## [1] 0.001276954
## [1] 0.001819537
## [1] 0.002298739
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 162
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004663584
## [1] 0.001860411
## [1] 0.001861598
## [1] 0.002477408
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 163
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003889828
## [1] 0.003757002
## [1] 0.004623227
## [1] 0.004522942
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 164
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004516159
## [1] 0.001641996
## [1] 0.002302387
## [1] 0.002709885
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 165
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003638785
## [1] 0.00125136
## [1] 0.001801767
## [1] 0.002192949
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 166
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00337657
## [1] 0.001522291
## [1] 0.002000719
## [1] 0.002213405
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 167
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004315398
## [1] 0.001678682
## [1] 0.002712649
## [1] 0.002920548
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 168
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003694279
## [1] 0.001563649
## [1] 0.002478916
## [1] 0.00248883
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 169
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004524952
## [1] 0.003390432
## [1] 0.00438233
## [1] 0.00467141
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 170
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004048359
## [1] 0.001379827
## [1] 0.001632329
## [1] 0.001908532
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 171
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004014016
## [1] 0.001921008
## [1] 0.002948123
## [1] 0.003201674
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 172
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00377172
## [1] 0.002335982
## [1] 0.003137667
## [1] 0.003177643
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 173
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003768297
## [1] 0.001367424
## [1] 0.002046437
## [1] 0.002390536
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 174
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004146856
## [1] 0.001171197
## [1] 0.001282148
## [1] 0.001694655
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 175
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004579766
## [1] 0.001603464
## [1] 0.002563769
## [1] 0.00292065
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 176
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004422653
## [1] 0.001310107
## [1] 0.001109837
## [1] 0.001269017
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 177
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004058076
## [1] 0.001606351
## [1] 0.002713418
## [1] 0.002914797
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 178
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004747358
## [1] 0.001870753
## [1] 0.002592938
## [1] 0.002933049
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 179
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004285743
## [1] 0.002057558
## [1] 0.003238373
## [1] 0.003551822
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 180
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003816017
## [1] 0.001921916
## [1] 0.002968398
## [1] 0.003185342
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 181
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003585308
## [1] 0.001737634
## [1] 0.00285354
## [1] 0.003075453
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 182
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004199191
## [1] 0.001447218
## [1] 0.002384369
## [1] 0.002602618
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 183
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004265777
## [1] 0.002543102
## [1] 0.003510357
## [1] 0.003670729
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 184
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005477778
## [1] 0.002390643
## [1] 0.001188435
## [1] 0.001572495
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 185
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004793339
## [1] 0.002831149
## [1] 0.003665253
## [1] 0.003932269
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 186
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003288641
## [1] 0.002191499
## [1] 0.00317631
## [1] 0.003243935
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 187
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004236043
## [1] 0.002106137
## [1] 0.003035395
## [1] 0.003191114
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 188
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004333485
## [1] 0.001674992
## [1] 0.002380278
## [1] 0.002477354
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 189
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004310947
## [1] 0.001576866
## [1] 0.002124635
## [1] 0.00250017
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 190
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004167496
## [1] 0.001498956
## [1] 0.002540452
## [1] 0.002688432
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 191
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004229348
## [1] 0.004536505
## [1] 0.00504064
## [1] 0.004904396
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 192
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004051099
## [1] 0.001489897
## [1] 0.002502341
## [1] 0.002654422
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 193
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004348723
## [1] 0.0021618
## [1] 0.003311782
## [1] 0.003587925
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 194
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003269959
## [1] 0.001714898
## [1] 0.002802164
## [1] 0.003061433
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 195
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004399184
## [1] 0.002973068
## [1] 0.003812089
## [1] 0.004009402
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 196
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004187221
## [1] 0.004823609
## [1] 0.005514904
## [1] 0.005599064
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 197
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004445114
## [1] 0.003503303
## [1] 0.004348697
## [1] 0.00448566
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 198
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003743431
## [1] 0.001650479
## [1] 0.002571204
## [1] 0.002796467
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 199
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003906257
## [1] 0.001273403
## [1] 0.001489136
## [1] 0.001621695
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 200
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00446325
## [1] 0.003363305
## [1] 0.004424157
## [1] 0.004670021
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 201
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004346634
## [1] 0.003120417
## [1] 0.003964276
## [1] 0.003992099
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 202
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003864149
## [1] 0.001114114
## [1] 0.00116855
## [1] 0.001444552
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 203
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003750185
## [1] 0.00120429
## [1] 0.002050897
## [1] 0.002193483
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 204
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004140854
## [1] 0.002186772
## [1] 0.003273111
## [1] 0.003612446
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 205
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004163882
## [1] 0.002557491
## [1] 0.003534161
## [1] 0.003751071
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 206
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004220175
## [1] 0.001527653
## [1] 0.0009371374
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 207
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004354989
## [1] 0.001492433
## [1] 0.001794803
## [1] 0.002110012
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 208
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004868067
## [1] 0.003300008
## [1] 0.004168526
## [1] 0.004438033
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 209
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004331976
## [1] 0.002388224
## [1] 0.003543298
## [1] 0.003808035
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 210
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004099116
## [1] 0.001586559
## [1] 0.002845268
## [1] 0.00323755
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 211
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003379196
## [1] 0.001575904
## [1] 0.002456929
## [1] 0.002652325
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 212
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00454087
## [1] 0.001759805
## [1] 0.0006201073
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 213
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003693125
## [1] 0.002863735
## [1] 0.003692523
## [1] 0.003749599
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 214
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004527638
## [1] 0.004046729
## [1] 0.004695658
## [1] 0.004684608
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 215
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003589507
## [1] 0.001919757
## [1] 0.00291736
## [1] 0.003105089
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 216
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004571578
## [1] 0.002233296
## [1] 0.003304299
## [1] 0.003599108
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 217
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003664145
## [1] 0.003525523
## [1] 0.004283678
## [1] 0.004395754
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 218
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004325815
## [1] 0.001703399
## [1] 0.002778152
## [1] 0.003030004
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 219
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004440085
## [1] 0.001587271
## [1] 0.002855758
## [1] 0.003276937
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 220
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003671065
## [1] 0.001454409
## [1] 0.0024328
## [1] 0.002541317
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 221
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00342033
## [1] 0.003174821
## [1] 0.003793127
## [1] 0.003889741
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 222
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00403257
## [1] 0.002595059
## [1] 0.003247085
## [1] 0.003289333
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 223
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003973529
## [1] 0.001495904
## [1] 0.002506077
## [1] 0.002794158
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 224
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004338852
## [1] 0.001563618
## [1] 0.002552331
## [1] 0.002752347
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 225
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002901783
## [1] 0.002639209
## [1] 0.003439884
## [1] 0.003352175
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 226
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003345747
## [1] 0.001725865
## [1] 0.002615876
## [1] 0.002784373
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 227
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00499945
## [1] 0.002150274
## [1] 0.003082934
## [1] 0.003473602
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 228
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003968077
## [1] 0.001397027
## [1] 0.002192525
## [1] 0.002562925
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 229
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003918392
## [1] 0.00162353
## [1] 0.002563981
## [1] 0.002790442
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 230
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005928277
## [1] 0.00212974
## [1] 0.000856821
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 231
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003874104
## [1] 0.001214346
## [1] 0.001964328
## [1] 0.002123814
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 232
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003311135
## [1] 0.00230532
## [1] 0.003046812
## [1] 0.003185833
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 233
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00441536
## [1] 0.00160929
## [1] 0.002112427
## [1] 0.002245044
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 234
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004127317
## [1] 0.001887237
## [1] 0.002783429
## [1] 0.002917721
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 235
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003543152
## [1] 0.002909566
## [1] 0.00361333
## [1] 0.003769131
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 236
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004056855
## [1] 0.003486468
## [1] 0.004269388
## [1] 0.004412808
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 237
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004536349
## [1] 0.001722443
## [1] 0.002450391
## [1] 0.002713077
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 238
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003771331
## [1] 0.004143758
## [1] 0.004701704
## [1] 0.004635635
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 239
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004608261
## [1] 0.003115379
## [1] 0.004126264
## [1] 0.004485804
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 240
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004255733
## [1] 0.001542072
## [1] 0.002144812
## [1] 0.002375959
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 241
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004200357
## [1] 0.001512634
## [1] 0.001227948
## [1] 0.001695871
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 242
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002949173
## [1] 0.001731209
## [1] 0.002742532
## [1] 0.002762236
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 243
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004787439
## [1] 0.001930527
## [1] 0.001272228
## [1] 0.001638369
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 244
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004980381
## [1] 0.003925318
## [1] 0.004841371
## [1] 0.005139595
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 245
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004247915
## [1] 0.001382099
## [1] 0.001987771
## [1] 0.002187309
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 246
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004459075
## [1] 0.001623058
## [1] 0.001306152
## [1] 0.001772765
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 247
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00406763
## [1] 0.001723377
## [1] 0.002617841
## [1] 0.002939994
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 248
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004492604
## [1] 0.002449269
## [1] 0.003196526
## [1] 0.003449997
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 249
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004419442
## [1] 0.002562827
## [1] 0.003313741
## [1] 0.003548524
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 250
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003988121
## [1] 0.00211709
## [1] 0.002755819
## [1] 0.002991149
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 251
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003244597
## [1] 0.0012957
## [1] 0.0021699
## [1] 0.002381099
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 252
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00502107
## [1] 0.00204611
## [1] 0.002310589
## [1] 0.002730097
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 253
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003464661
## [1] 0.001991076
## [1] 0.002805132
## [1] 0.002877956
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 254
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004314357
## [1] 0.001460142
## [1] 0.001862191
## [1] 0.002270385
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 255
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00367985
## [1] 0.001643245
## [1] 0.002579861
## [1] 0.002753814
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 256
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003210963
## [1] 0.002427102
## [1] 0.003257102
## [1] 0.003395092
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 257
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004118852
## [1] 0.001773017
## [1] 0.002864606
## [1] 0.003228903
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 258
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005527752
## [1] 0.003314443
## [1] 0.003950316
## [1] 0.004041344
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 259
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004287202
## [1] 0.001891122
## [1] 0.002716749
## [1] 0.002982476
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 260
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004673998
## [1] 0.001892348
## [1] 0.002625916
## [1] 0.002888151
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 261
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004168294
## [1] 0.001273888
## [1] 0.002225951
## [1] 0.002537826
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 262
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003031161
## [1] 0.002880876
## [1] 0.003445256
## [1] 0.003519988
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 263
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003883367
## [1] 0.002208342
## [1] 0.002916742
## [1] 0.003129838
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 264
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003352516
## [1] 0.002730777
## [1] 0.003417238
## [1] 0.003567452
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 265
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003757442
## [1] 0.001284097
## [1] 0.002164876
## [1] 0.002545843
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 266
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004442038
## [1] 0.001847137
## [1] 0.002400638
## [1] 0.002667032
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 267
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003272581
## [1] 0.001480001
## [1] 0.001362368
## [1] 0.00124558
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 268
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003814378
## [1] 0.001615539
## [1] 0.001510669
## [1] 0.001292836
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 269
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003026156
## [1] 0.001559917
## [1] 0.002164865
## [1] 0.001984748
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 270
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002938152
## [1] 0.001660803
## [1] 0.002207232
## [1] 0.001932378
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 271
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003746433
## [1] 0.001799591
## [1] 0.002732836
## [1] 0.002872517
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 272
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005564265
## [1] 0.001404555
## [1] 0.001205323
## [1] 0.001162709
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 273
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003233348
## [1] 0.001375451
## [1] 0.001225191
## [1] 0.001118603
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 274
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00412556
## [1] 0.001459679
## [1] 0.00125666
## [1] 0.001078579
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 275
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00291069
## [1] 0.001534596
## [1] 0.001230036
## [1] 0.00138191
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 276
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00671091
## [1] 0.001864932
## [1] 0.0009593467
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 277
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002580566
## [1] 0.002555766
## [1] 0.003064051
## [1] 0.002923599
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 278
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00596959
## [1] 0.001383875
## [1] 0.001078839
## [1] 0.0009673703
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 279
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003615575
## [1] 0.001373231
## [1] 0.001753189
## [1] 0.001899357
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 280
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006242491
## [1] 0.001511329
## [1] 0.001186086
## [1] 0.001027055
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 281
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00265254
## [1] 0.002224042
## [1] 0.0026619
## [1] 0.002188346
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 282
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002114022
## [1] 0.002476136
## [1] 0.002813103
## [1] 0.002341702
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 283
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003384068
## [1] 0.00161357
## [1] 0.00141189
## [1] 0.001238619
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 284
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003466996
## [1] 0.001625684
## [1] 0.002263933
## [1] 0.002027927
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 285
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002754151
## [1] 0.001621992
## [1] 0.002193352
## [1] 0.001990059
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 286
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003338995
## [1] 0.001443685
## [1] 0.001874134
## [1] 0.002009198
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 287
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002821964
## [1] 0.001689271
## [1] 0.00208245
## [1] 0.00179023
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 288
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003683489
## [1] 0.001331987
## [1] 0.001322764
## [1] 0.001414944
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 289
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002974181
## [1] 0.001601752
## [1] 0.001368108
## [1] 0.001383979
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 290
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002892473
## [1] 0.001540088
## [1] 0.001619831
## [1] 0.001545348
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 291
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005099709
## [1] 0.00139563
## [1] 0.001196148
## [1] 0.001347324
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 292
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003091912
## [1] 0.001451347
## [1] 0.001733369
## [1] 0.001613475
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 293
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003551036
## [1] 0.001354391
## [1] 0.00192833
## [1] 0.002164806
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 294
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003043198
## [1] 0.002535579
## [1] 0.00305673
## [1] 0.002542663
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 295
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004426729
## [1] 0.0013805
## [1] 0.001300059
## [1] 0.001119156
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 296
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002694653
## [1] 0.00178813
## [1] 0.00304142
## [1] 0.002970353
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 297
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002611157
## [1] 0.001612457
## [1] 0.001493176
## [1] 0.001327268
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 298
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004651315
## [1] 0.001477726
## [1] 0.001324661
## [1] 0.001499917
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 299
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007388787
## [1] 0.002388588
## [1] 0.001062996
## [1] 0.001073934
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 300
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00345358
## [1] 0.001491473
## [1] 0.002376554
## [1] 0.002395371
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 301
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003779421
## [1] 0.001433018
## [1] 0.001160256
## [1] 0.001023758
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 302
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00387591
## [1] 0.001431328
## [1] 0.001248078
## [1] 0.001095055
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 303
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002354229
## [1] 0.001587228
## [1] 0.00158072
## [1] 0.001185288
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 304
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004005453
## [1] 0.001271644
## [1] 0.001223675
## [1] 0.001061459
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 305
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003005433
## [1] 0.002555327
## [1] 0.003254381
## [1] 0.002947629
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 306
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006496011
## [1] 0.001403513
## [1] 0.001304138
## [1] 0.001128009
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 307
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003606967
## [1] 0.001425803
## [1] 0.002269441
## [1] 0.002346494
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 308
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002788548
## [1] 0.001424366
## [1] 0.001574762
## [1] 0.001184224
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 309
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004723298
## [1] 0.001205665
## [1] 0.001157074
## [1] 0.001180721
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 310
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004972466
## [1] 0.001032848
## [1] 0.00102058
## [1] 0.000956546
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 311
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003562327
## [1] 0.001087013
## [1] 0.001112406
## [1] 0.00132417
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 312
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004968534
## [1] 0.0016351
## [1] 0.000933658
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 313
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003796428
## [1] 0.001072735
## [1] 0.001799646
## [1] 0.002008036
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 314
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003857301
## [1] 0.00118075
## [1] 0.001981689
## [1] 0.002107299
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 315
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003731313
## [1] 0.001149002
## [1] 0.001348019
## [1] 0.001656109
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 316
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004444856
## [1] 0.001723071
## [1] 0.001643431
## [1] 0.00200646
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 317
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004862466
## [1] 0.001920042
## [1] 0.0009954002
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 318
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003818516
## [1] 0.001714108
## [1] 0.002487796
## [1] 0.002578841
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 319
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004146882
## [1] 0.001391105
## [1] 0.00110637
## [1] 0.00125253
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 320
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003075779
## [1] 0.0015004
## [1] 0.002156659
## [1] 0.00229608
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 321
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00458257
## [1] 0.001231081
## [1] 0.0009538959
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 322
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005279731
## [1] 0.001782109
## [1] 0.0008353057
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 323
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003840115
## [1] 0.001093338
## [1] 0.001118597
## [1] 0.001194707
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 324
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003681496
## [1] 0.00105581
## [1] 0.001109227
## [1] 0.001458774
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 325
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004140589
## [1] 0.001105659
## [1] 0.001092296
## [1] 0.0009780408
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 326
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003209848
## [1] 0.001116826
## [1] 0.001528447
## [1] 0.001649703
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 327
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003886437
## [1] 0.001456206
## [1] 0.002022796
## [1] 0.00211254
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 328
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003757112
## [1] 0.001431022
## [1] 0.001829305
## [1] 0.001813458
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 329
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003669607
## [1] 0.001406633
## [1] 0.001556883
## [1] 0.001733067
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 330
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003734937
## [1] 0.001342422
## [1] 0.002148305
## [1] 0.002239309
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 331
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003645217
## [1] 0.001423323
## [1] 0.001356038
## [1] 0.001278576
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 332
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003530944
## [1] 0.001609394
## [1] 0.001355474
## [1] 0.001185824
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 333
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004196098
## [1] 0.001727061
## [1] 0.002423354
## [1] 0.002367512
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 334
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003506657
## [1] 0.002407806
## [1] 0.003070104
## [1] 0.00288584
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 335
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00376865
## [1] 0.001613142
## [1] 0.001521434
## [1] 0.001439039
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 336
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004498999
## [1] 0.001577382
## [1] 0.002436638
## [1] 0.00250626
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 337
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003466314
## [1] 0.001556705
## [1] 0.001762848
## [1] 0.001877243
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 338
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003165172
## [1] 0.001449668
## [1] 0.001842265
## [1] 0.00187385
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 339
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003485013
## [1] 0.001373326
## [1] 0.001319255
## [1] 0.001481672
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 340
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0034658
## [1] 0.001387039
## [1] 0.002035432
## [1] 0.002250127
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 341
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003020254
## [1] 0.001684269
## [1] 0.001983474
## [1] 0.001710608
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 342
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002967454
## [1] 0.001505939
## [1] 0.002349659
## [1] 0.002347197
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 343
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004594546
## [1] 0.001290834
## [1] 0.001179419
## [1] 0.0009994061
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 344
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003062351
## [1] 0.001273327
## [1] 0.001763569
## [1] 0.001803734
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 345
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003164855
## [1] 0.00197119
## [1] 0.00273652
## [1] 0.002514359
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 346
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003482521
## [1] 0.002040083
## [1] 0.002701058
## [1] 0.002551202
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 347
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002048468
## [1] 0.002215297
## [1] 0.002686745
## [1] 0.00266197
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 348
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002031614
## [1] 0.001728927
## [1] 0.001847409
## [1] 0.001559994
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 349
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00274341
## [1] 0.001719966
## [1] 0.001776813
## [1] 0.001790128
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 350
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002094383
## [1] 0.001577357
## [1] 0.002033332
## [1] 0.002009475
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 351
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00268111
## [1] 0.001814664
## [1] 0.002570851
## [1] 0.002657114
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 352
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002639251
## [1] 0.001795024
## [1] 0.002336047
## [1] 0.002265932
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 353
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00185581
## [1] 0.003538912
## [1] 0.003782186
## [1] 0.003400296
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 354
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002276897
## [1] 0.002678697
## [1] 0.00309633
## [1] 0.002576198
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 355
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003645356
## [1] 0.003649711
## [1] 0.004135724
## [1] 0.003758281
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 356
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002547255
## [1] 0.003029644
## [1] 0.00360824
## [1] 0.003422978
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 357
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002710965
## [1] 0.003216663
## [1] 0.003845505
## [1] 0.00373382
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 358
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002268893
## [1] 0.003218912
## [1] 0.003816851
## [1] 0.003660028
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 359
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003507031
## [1] 0.002441438
## [1] 0.002970615
## [1] 0.002787731
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 360
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003439097
## [1] 0.001687912
## [1] 0.001725301
## [1] 0.001650515
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 361
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003571297
## [1] 0.002082437
## [1] 0.003032762
## [1] 0.003152755
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 362
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003242976
## [1] 0.001689903
## [1] 0.002603877
## [1] 0.002676094
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 363
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003766381
## [1] 0.003067258
## [1] 0.003758236
## [1] 0.003801181
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 364
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003728647
## [1] 0.002208057
## [1] 0.0030224
## [1] 0.003019982
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 365
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002672735
## [1] 0.00242128
## [1] 0.002932137
## [1] 0.002940061
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 366
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004088338
## [1] 0.002858299
## [1] 0.003675338
## [1] 0.003710179
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 367
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004350275
## [1] 0.003210226
## [1] 0.003963989
## [1] 0.00395053
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 368
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004046512
## [1] 0.002154643
## [1] 0.003092779
## [1] 0.003266773
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 369
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003832704
## [1] 0.003683493
## [1] 0.004574084
## [1] 0.004708998
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 370
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003486984
## [1] 0.002887832
## [1] 0.003607361
## [1] 0.003503459
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 371
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002985638
## [1] 0.00246737
## [1] 0.00303464
## [1] 0.002977655
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 372
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003043257
## [1] 0.002294238
## [1] 0.003070196
## [1] 0.003131619
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 373
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003465811
## [1] 0.002863745
## [1] 0.003514036
## [1] 0.003287863
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 374
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00274197
## [1] 0.003414076
## [1] 0.004076839
## [1] 0.004040382
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 375
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003157827
## [1] 0.001435316
## [1] 0.001713859
## [1] 0.001867855
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 376
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002109525
## [1] 0.001558863
## [1] 0.001566625
## [1] 0.001697922
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 377
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003641764
## [1] 0.001551443
## [1] 0.002284809
## [1] 0.002380606
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 378
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002932951
## [1] 0.003096895
## [1] 0.00362268
## [1] 0.003552491
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 379
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003243551
## [1] 0.002820201
## [1] 0.003372036
## [1] 0.003241678
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 380
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004122299
## [1] 0.002060818
## [1] 0.003135588
## [1] 0.003164996
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 381
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002318646
## [1] 0.001782107
## [1] 0.002578828
## [1] 0.002623859
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 382
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003006285
## [1] 0.003507268
## [1] 0.004362586
## [1] 0.004554704
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 383
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002533117
## [1] 0.001399324
## [1] 0.001867133
## [1] 0.001776749
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 384
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002577229
## [1] 0.002118972
## [1] 0.002851791
## [1] 0.002960102
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 385
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00344416
## [1] 0.002178815
## [1] 0.003048648
## [1] 0.003208457
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 386
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003728194
## [1] 0.001622375
## [1] 0.001736769
## [1] 0.001530449
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 387
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002139283
## [1] 0.001753924
## [1] 0.002560569
## [1] 0.002565973
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 388
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002383736
## [1] 0.002243755
## [1] 0.00304898
## [1] 0.003228723
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 389
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003482621
## [1] 0.001954967
## [1] 0.002922134
## [1] 0.00298707
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 390
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002002563
## [1] 0.001481209
## [1] 0.002151547
## [1] 0.002245863
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 391
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00266621
## [1] 0.003024626
## [1] 0.003551521
## [1] 0.003557806
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 392
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003637341
## [1] 0.001625613
## [1] 0.002698155
## [1] 0.002771033
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 393
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003171681
## [1] 0.001497309
## [1] 0.001375147
## [1] 0.001184899
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 394
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003043693
## [1] 0.002316958
## [1] 0.002962263
## [1] 0.003073954
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 395
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002733198
## [1] 0.001993262
## [1] 0.002776924
## [1] 0.002930682
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 396
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00428364
## [1] 0.003692767
## [1] 0.004394612
## [1] 0.004675484
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 397
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003282919
## [1] 0.0033608
## [1] 0.003894465
## [1] 0.004028997
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 398
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002695027
## [1] 0.001490639
## [1] 0.002322572
## [1] 0.002591427
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 399
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003759416
## [1] 0.001518698
## [1] 0.002548559
## [1] 0.002781566
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 400
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0014974
## [1] 0.001026543
## [1] 0.001115966
## [1] 0.001222516
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 401
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002665957
## [1] 0.001681125
## [1] 0.002239159
## [1] 0.002368164
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 402
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00400256
## [1] 0.003055362
## [1] 0.003740815
## [1] 0.003905095
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 403
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004703487
## [1] 0.00287596
## [1] 0.003705487
## [1] 0.003878288
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 404
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004400285
## [1] 0.00148003
## [1] 0.001489767
## [1] 0.001851124
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 405
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003978367
## [1] 0.001939309
## [1] 0.002917716
## [1] 0.003080422
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 406
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003353116
## [1] 0.001386009
## [1] 0.001596208
## [1] 0.001885392
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 407
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002480609
## [1] 0.001937416
## [1] 0.002711144
## [1] 0.00290429
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 408
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003812124
## [1] 0.0016801
## [1] 0.002825062
## [1] 0.003071082
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 409
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00436289
## [1] 0.003252585
## [1] 0.004263802
## [1] 0.004486485
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 410
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002346176
## [1] 0.003206894
## [1] 0.003630288
## [1] 0.003736333
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 411
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004410438
## [1] 0.001562058
## [1] 0.001925876
## [1] 0.002251955
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 412
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003833374
## [1] 0.002752283
## [1] 0.003660126
## [1] 0.003770777
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 413
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004360448
## [1] 0.002484744
## [1] 0.003437583
## [1] 0.003680479
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 414
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002191753
## [1] 0.002381718
## [1] 0.003161837
## [1] 0.003208208
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 415
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0009898895
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 416
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001815393
## [1] 0.002879661
## [1] 0.00348555
## [1] 0.003410473
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 417
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004130476
## [1] 0.001525508
## [1] 0.001763171
## [1] 0.00220156
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 418
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004124445
## [1] 0.002868171
## [1] 0.004022905
## [1] 0.004376598
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 419
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002519332
## [1] 0.003261702
## [1] 0.003805709
## [1] 0.003829444
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 420
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002500195
## [1] 0.001629003
## [1] 0.002580985
## [1] 0.002921144
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 421
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002779667
## [1] 0.002377521
## [1] 0.003173009
## [1] 0.003347698
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 422
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003334903
## [1] 0.0024947
## [1] 0.003340549
## [1] 0.003451699
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 423
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003740841
## [1] 0.003024325
## [1] 0.003576623
## [1] 0.003745989
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 424
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002007273
## [1] 0.002135306
## [1] 0.002603125
## [1] 0.0027133
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 425
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003307297
## [1] 0.00497415
## [1] 0.005410346
## [1] 0.005194341
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 426
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003725755
## [1] 0.002217177
## [1] 0.003163556
## [1] 0.003408586
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 427
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004448711
## [1] 0.003822296
## [1] 0.004734067
## [1] 0.004958272
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 428
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003137127
## [1] 0.001755255
## [1] 0.002598787
## [1] 0.002543024
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 429
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003441298
## [1] 0.003298076
## [1] 0.003689642
## [1] 0.003778162
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 430
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003837805
## [1] 0.002968363
## [1] 0.003826063
## [1] 0.004204339
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 431
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004661996
## [1] 0.002532147
## [1] 0.00360325
## [1] 0.003930156
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 432
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002361066
## [1] 0.002289926
## [1] 0.003098853
## [1] 0.003336119
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 433
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004286909
## [1] 0.004201603
## [1] 0.005301425
## [1] 0.005542011
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 434
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002366883
## [1] 0.002703042
## [1] 0.003189564
## [1] 0.003000768
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 435
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004425718
## [1] 0.00296142
## [1] 0.003933977
## [1] 0.004308805
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 436
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001670841
## [1] 0.002318419
## [1] 0.002698081
## [1] 0.002760677
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 437
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004275235
## [1] 0.001559015
## [1] 0.000611572
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 438
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003553212
## [1] 0.001412135
## [1] 0.001473465
## [1] 0.00171533
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 439
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001082099
## [1] 0.001420602
## [1] 0.001830782
## [1] 0.001823838
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 440
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.000784151
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 441
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004264386
## [1] 0.004218916
## [1] 0.005153252
## [1] 0.005328188
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 442
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0008109698
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 443
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002601169
## [1] 0.002759995
## [1] 0.003492475
## [1] 0.003617761
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 444
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00390131
## [1] 0.003607701
## [1] 0.00440204
## [1] 0.004491978
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 445
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0014396
## [1] 0.002344238
## [1] 0.002864816
## [1] 0.003039919
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 446
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002420322
## [1] 0.001939512
## [1] 0.002826339
## [1] 0.003021541
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 447
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004070252
## [1] 0.001360256
## [1] 0.00141274
## [1] 0.001745231
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 448
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003581036
## [1] 0.003101441
## [1] 0.003662917
## [1] 0.003729193
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 449
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004113002
## [1] 0.003375746
## [1] 0.004115582
## [1] 0.00436177
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 450
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003582055
## [1] 0.002471259
## [1] 0.003081597
## [1] 0.003219164
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 451
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004727792
## [1] 0.001844294
## [1] 0.002228257
## [1] 0.002375593
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 452
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004131542
## [1] 0.001418048
## [1] 0.001779633
## [1] 0.00195128
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 453
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004594861
## [1] 0.001723441
## [1] 0.001075128
## [1] 0.001416034
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 454
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004243596
## [1] 0.001916898
## [1] 0.002501434
## [1] 0.002346568
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 455
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003927884
## [1] 0.001839265
## [1] 0.002840285
## [1] 0.002854598
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 456
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00400328
## [1] 0.003027782
## [1] 0.00361858
## [1] 0.003500886
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 457
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005870842
## [1] 0.001383394
## [1] 0.0009740405
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 458
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004161844
## [1] 0.001384978
## [1] 0.001152854
## [1] 0.001303673
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 459
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004365635
## [1] 0.001637749
## [1] 0.002415419
## [1] 0.002513319
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 460
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004568206
## [1] 0.001688223
## [1] 0.001844771
## [1] 0.002169832
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 461
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004040195
## [1] 0.002394089
## [1] 0.003231061
## [1] 0.003148067
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 462
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004321434
## [1] 0.001477669
## [1] 0.001141606
## [1] 0.00143759
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 463
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004615503
## [1] 0.001857407
## [1] 0.002457643
## [1] 0.002669167
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 464
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003858938
## [1] 0.001369567
## [1] 0.001821454
## [1] 0.002020011
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 465
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004567113
## [1] 0.001673548
## [1] 0.001133522
## [1] 0.001255035
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 466
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004948355
## [1] 0.002056405
## [1] 0.001827118
## [1] 0.002123052
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 467
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004498426
## [1] 0.001630227
## [1] 0.001487076
## [1] 0.001832085
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 468
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004355635
## [1] 0.001597394
## [1] 0.002655648
## [1] 0.002640389
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 469
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004344207
## [1] 0.001700172
## [1] 0.002821214
## [1] 0.002887327
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 470
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004557141
## [1] 0.002682466
## [1] 0.003624156
## [1] 0.003549989
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 471
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004815789
## [1] 0.002002402
## [1] 0.00236428
## [1] 0.002557365
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 472
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004693601
## [1] 0.001327589
## [1] 0.001187051
## [1] 0.001238074
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 473
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004025425
## [1] 0.002337979
## [1] 0.003177565
## [1] 0.003152805
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 474
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0042345
## [1] 0.001441769
## [1] 0.001058151
## [1] 0.001007074
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 475
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004447411
## [1] 0.003752678
## [1] 0.004463395
## [1] 0.004305607
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 476
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.008012604
## [1] 0.002867652
## [1] 0.0008441319
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 477
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.01056392
## [1] 0.003698594
## [1] 0.001230149
## [1] 0.0006526983
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 478
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006485516
## [1] 0.001456922
## [1] 0.0009227285
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 479
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.009487619
## [1] 0.003040236
## [1] 0.001110052
## [1] 0.00070651
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 480
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.009339607
## [1] 0.003907311
## [1] 0.002195302
## [1] 0.001725259
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 481
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005224103
## [1] 0.002071877
## [1] 0.001744266
## [1] 0.002059815
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 482
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005237509
## [1] 0.002077478
## [1] 0.00207462
## [1] 0.002345634
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 483
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004672166
## [1] 0.001750289
## [1] 0.002239718
## [1] 0.002342426
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 484
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004438404
## [1] 0.00166316
## [1] 0.002066
## [1] 0.002263665
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 485
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.007190501
## [1] 0.003402772
## [1] 0.001981612
## [1] 0.002287299
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 486
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001266725
## [1] 0.003167707
## [1] 0.003092859
## [1] 0.0021129
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 487
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001979418
## [1] 0.005272862
## [1] 0.005455865
## [1] 0.004610392
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 488
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003581675
## [1] 0.0009086231
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 489
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00339406
## [1] 0.001063142
## [1] 0.001881406
## [1] 0.001699753
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 490
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002654635
## [1] 0.001720343
## [1] 0.002830817
## [1] 0.002729854
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 491
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004204856
## [1] 0.0009157328
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 492
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003049839
## [1] 0.001140245
## [1] 0.001907873
## [1] 0.001536073
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 493
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002320979
## [1] 0.001915167
## [1] 0.002779586
## [1] 0.002503502
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 494
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001305189
## [1] 0.002969148
## [1] 0.002961251
## [1] 0.00200907
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 495
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004455034
## [1] 0.0009017618
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 496
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003133698
## [1] 0.001656013
## [1] 0.002818886
## [1] 0.002817676
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 497
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003379454
## [1] 0.002669651
## [1] 0.003553439
## [1] 0.003404562
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 498
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005463625
## [1] 0.001091096
## [1] 0.001101846
## [1] 0.0009867199
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 499
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004671456
## [1] 0.002021282
## [1] 0.00166729
## [1] 0.002108438
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 500
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005229675
## [1] 0.002199003
## [1] 0.001519566
## [1] 0.002224384
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 501
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004412589
## [1] 0.001842823
## [1] 0.002473304
## [1] 0.002870857
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 502
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005166842
## [1] 0.001119346
## [1] 0.001161917
## [1] 0.001625063
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 503
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004103174
## [1] 0.001553467
## [1] 0.001786394
## [1] 0.002136875
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 504
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005803069
## [1] 0.001843526
## [1] 0.001085972
## [1] 0.00165987
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 505
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004422512
## [1] 0.00186814
## [1] 0.002392563
## [1] 0.00288891
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 506
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.01875432
## [1] 0.01134179
## [1] 0.007976834
## [1] 0.006251892
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 507
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005231642
## [1] 0.002640797
## [1] 0.004561799
## [1] 0.00535209
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 508
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.01069722
## [1] 0.004105697
## [1] 0.001521292
## [1] 0.0007634926
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 509
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003679975
## [1] 0.00252503
## [1] 0.003063871
## [1] 0.003951733
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 510
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001420577
## [1] 0.002968258
## [1] 0.00210513
## [1] 0.001313745
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 511
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002775557
## [1] 0.001461895
## [1] 0.001537284
## [1] 0.001455171
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 512
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005153617
## [1] 0.003452465
## [1] 0.003444178
## [1] 0.003847647
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 513
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002559091
## [1] 0.002063615
## [1] 0.002324252
## [1] 0.001807746
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 514
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005323323
## [1] 0.00402323
## [1] 0.004486601
## [1] 0.004911035
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 515
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001292748
## [1] 0.001355773
## [1] 0.001503572
## [1] 0.001484863
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 516
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0048332
## [1] 0.00308168
## [1] 0.002791429
## [1] 0.002868919
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 517
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003491111
## [1] 0.001977197
## [1] 0.0018766
## [1] 0.002075102
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 518
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005359524
## [1] 0.002722447
## [1] 0.002430981
## [1] 0.002712783
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 519
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002319844
## [1] 0.001635475
## [1] 0.001642707
## [1] 0.002015956
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 520
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002184724
## [1] 0.001576033
## [1] 0.001667243
## [1] 0.001582371
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 521
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003942681
## [1] 0.002611548
## [1] 0.002359133
## [1] 0.002333333
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 522
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004070011
## [1] 0.001479433
## [1] 0.001607853
## [1] 0.001877762
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 523
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006847198
## [1] 0.0024024
## [1] 0.001284316
## [1] 0.00114481
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 524
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006160567
## [1] 0.00178464
## [1] 0.001091311
## [1] 0.000992835
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 525
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003675536
## [1] 0.001202325
## [1] 0.001401117
## [1] 0.001770069
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 526
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005491278
## [1] 0.001297469
## [1] 0.001248526
## [1] 0.001133969
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 527
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.0009597291
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 528
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005785998
## [1] 0.002116727
## [1] 0.0007223796
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 529
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.006605343
## [1] 0.004142326
## [1] 0.003683055
## [1] 0.003753593
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 530
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004465868
## [1] 0.001007271
## [1] 0.00120331
## [1] 0.00121629
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 531
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001203342
## [1] 0.001280938
## [1] 0.001361344
## [1] 0.001293763
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 532
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002209166
## [1] 0.001483483
## [1] 0.001530571
## [1] 0.001394337
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 533
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004984648
## [1] 0.002334127
## [1] 0.002546833
## [1] 0.003279834
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 534
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001656887
## [1] 0.001439694
## [1] 0.001482359
## [1] 0.001362296
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 535
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005886423
## [1] 0.002012803
## [1] 0.001319791
## [1] 0.001529018
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 536
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004014744
## [1] 0.0009506922
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 537
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.005219194
## [1] 0.002618662
## [1] 0.002789129
## [1] 0.003492718
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 538
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001661055
## [1] 0.001447109
## [1] 0.001465851
## [1] 0.001381868
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 539
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002312138
## [1] 0.001470543
## [1] 0.001541999
## [1] 0.001442173
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 540
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.002668233
## [1] 0.001504777
## [1] 0.001532107
## [1] 0.002175353
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 541
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.000967094
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 542
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001439247
## [1] 0.001730975
## [1] 0.001701303
## [1] 0.002342692
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 543
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003008895
## [1] 0.001485359
## [1] 0.001547939
## [1] 0.001474236
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 544
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003792766
## [1] 0.002028236
## [1] 0.002290341
## [1] 0.003005674
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 545
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003315612
## [1] 0.001499638
## [1] 0.001549775
## [1] 0.001835902
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 546
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.001484957
## [1] 0.001763264
## [1] 0.001690037
## [1] 0.001550756
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 547
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003167052
## [1] 0.001480889
## [1] 0.001521513
## [1] 0.002175147
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 548
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00371207
## [1] 0.002175611
## [1] 0.002453219
## [1] 0.003226956
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 549
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.00144899
## [1] 0.001575316
## [1] 0.001577266
## [1] 0.001456822
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 550
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.004484488
## [1] 0.002259194
## [1] 0.002253491
## [1] 0.002752854
## [1] "Done"
## [1] "Start normalising input probes"
## ii= 551
## [1] "Fitting EM beta mixture to input probes"
## [1] Inf
## [1] 0.003812476
## [1] 0.001341613
## [1] 0.001417182
## [1] 0.001338861
## [1] "Done"
## [1] "Start normalising input probes"
# calibrate data from different tissue types separately
# normCali_BMof8TissueTypes <- CalibrateFUN2(GoldStaStudy = "GSE74738")
saveRDS(normCali_BMof9TissueTypes_CaliTogether,
file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/normCali_BMof9TissueTypes_CaliTogether.rds")
plotMDSFUNTissue argument in plotMDSFUN function could be: Placenta, Amnion, Chorion, Decidua, Maternal whole blood, placental mesenchyme, placental trophoblast, umbilical cord, Umbilical cord blood.
# phenoData: GEO_phenotypes, meta data for all samples
# Array: "450k" or "EPIC"
plotMDSFUN <- function(Normal_betaNorm, Tissue, PhenoData, ...){
registerDoParallel(cores = 10)
# get meta data
GEO_phenotypes_Tissue <- PhenoData %>%
filter(str_detect(Sample, pattern=paste0("^", Tissue, "$")))
# then get beta values for each tissue type
Normal_betaNorm_forPlot <- Normal_betaNorm[,colnames(Normal_betaNorm)%in%GEO_phenotypes_Tissue$Sample_name, drop=FALSE]
# plotMDS plots
if(all(table(GEO_phenotypes_Tissue$Sample_name==colnames(Normal_betaNorm_forPlot)))){
label <- GEO_phenotypes_Tissue$Trimester
}else{
print("Rownames of beta matrix were not matched with phenoData$Sample_name")
}
if(ncol(Normal_betaNorm_forPlot)>=3){
par(mfrow=c(1,1), ...)
plotMDS(Normal_betaNorm_forPlot, top=nrow(Normal_betaNorm_forPlot),
main=Tissue, labels= label, gene.selection="common")
}
# labels= label, col= pal[factor(label)],
# plot density plot anagin with other 96 samples
par(mfrow=c(1,1), cex=0.8, ...)
densityPlot(Normal_betaNorm_forPlot, sampGroups = label,
main=Tissue, xlab = "Normalised Beta values")
}# end function
plotMDSFUN, plot 9 separate plots for 9 different tissue types.TissueBMvalInfo <- tibble(
TissueTypes = c("Placenta", "Amnion", "Chorion", "Decidua",
"Maternal whole blood",
"placental mesenchyme",
"placental trophoblast", "umbilical cord", "Umbilical cord blood")
)
# use plotMDSFUN function
for(i in TissueBMvalInfo$TissueTypes){
plotMDSFUN(Normal_betaNorm = normCali_BMof9TissueTypes_CaliTogether$Beta,
Tissue = i,
PhenoData = normCali_BMof9TissueTypes_CaliTogether$BetaPhenoData)
}
plotAll function# value-- Beta or M
# TissueBMvalInfo -- a tibble containing BM names
plotAll <- function(BMvalue, GEO_phenotypes_joinedSamples){
registerDoParallel(cores = 10)
#plotMDS plots
## phenodata for these samples
GEO_phenotypes_551 <- GEO_phenotypes_joinedSamples[match(colnames(BMvalue),
GEO_phenotypes_joinedSamples$Sample_name),]
## check names all in same order or not
table(colnames(BMvalue)==GEO_phenotypes_551$Sample_name)
## plot MDS plot
par(mfrow=c(1,1))
MDS_norm551 <- plotMDS(BMvalue, top=nrow(BMvalue), labels= GEO_phenotypes_551$Sample,
gene.selection="common")
# plot density plot
par(mfrow=c(1,1), cex=0.8)
densityPlot(BMvalue, sampGroups = GEO_phenotypes_551$Sample, xlab = "Normalised Beta values")
# return Join.df_v2, GEO_phenotypes_norm551 and MDS_norm551
output_List <- list(JoinAll=BMvalue, phenoDataAll=GEO_phenotypes_551, MDSnorm551=MDS_norm551)
return(output_List)
}
plotAll functionMDSnormCali551_Beta <- plotAll(BMvalue = normCali_BMof9TissueTypes_CaliTogether$Beta,
GEO_phenotypes_joinedSamples = normCali_BMof9TissueTypes_CaliTogether$BetaPhenoData)
MDSnormCali551_M <- plotAll(BMvalue = normCali_BMof9TissueTypes_CaliTogether$M,
GEO_phenotypes_joinedSamples = normCali_BMof9TissueTypes_CaliTogether$BetaPhenoData)
save(MDSnormCali551_Beta, MDSnormCali551_M,
file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/GEO_joinedSamplesNormalisedCalibrated551_BetaM_MDS.RData")
ggplotggplotMDS functionlibrary(RColorBrewer)
colorFun <- colorRampPalette(brewer.pal(9, "Set1"))
pal2 <- colorFun(13)
# set up df for ggplot
## check sample orders were the same or not
table(colnames(MDSnormCali551_Beta$JoinAll)==MDSnormCali551_Beta$phenoDataAll$Sample_name)
##
## TRUE
## 551
table(colnames(MDSnormCali551_M$JoinAll)==MDSnormCali551_M$phenoDataAll$Sample_name)
##
## TRUE
## 551
# ggplotMDS function
## value -- Beta or M
ggplotMDS <- function(MDS_norm551, GEO_phenotypes_norm551, value){
new_plotDF <- data.frame(MDS_norm551$x,
MDS_norm551$y,
GA = GEO_phenotypes_norm551$Gestation,
FetalSex= GEO_phenotypes_norm551$Fetal_Sex,
Tissue=str_replace_all(GEO_phenotypes_norm551$Sample, c(
"placental"="Placental",
"umbilical"="Umbilical")),
Trimester=GEO_phenotypes_norm551$Trimester,
Study=GEO_phenotypes_norm551$Study,
Outlier=ifelse(GEO_phenotypes_norm551$Additional_Info%in%"Outlier", "Outlier", "Standard"),
ArrayType=GEO_phenotypes_norm551$ArrayType
)
colnames(new_plotDF) <- c("x", "y", "Gestational age", "FetalSex", "Tissue", "Trimester", "Study", "Outlier", "ArrayType")
# Plot the new dataframe
## color to use
namedPal2 <- pal2 %>% `names<-`(unique(new_plotDF$Tissue))
TissueShape <- factor(new_plotDF$Tissue)
MDSplot_norm551 <- new_plotDF %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Study, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(new_plotDF$Study))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=20))
# axis.text.x = element_text(angle=90, hjust=1))
# save the MDS plot as pdf:
pdf(file = paste0("/home/qianhui/DNAme/Process_decidual/figures/MDSplot-Normalised", value, "_joinedGEOsamples551.pdf"),
width = 13, height = 7)
theme_set(theme_bw())
MDSplot_norm551
dev.off()
# save as tiff
tiff(file = paste0("/home/qianhui/DNAme/Process_decidual/figures/MDSplot-Normalised", value, "_joinedGEOsamples551.tiff"),
width = 20,height = 15, units="cm", res = 300)
theme_set(theme_bw())
MDSplot_norm551
dev.off()
# show the plot
theme_set(theme_bw())
MDSplot_norm551 %>% print()
# return new_plotDF
return(new_plotDF)
}
ggplotMDS function# for MDSnormCali551_Beta
AllBetaMDSinfo <- ggplotMDS(MDS_norm551 = MDSnormCali551_Beta$MDSnorm551,
GEO_phenotypes_norm551 = MDSnormCali551_Beta$phenoDataAll,
value = "Beta")
AllBetaMDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(AllBetaMDSinfo$Study))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# for MDSnormCali551_M
AllMMDSinfo <- ggplotMDS(MDS_norm551 = MDSnormCali551_M$MDSnorm551,
GEO_phenotypes_norm551 = MDSnormCali551_M$phenoDataAll,
value = "M")
AllMMDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(AllMMDSinfo$Study))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
CombatFUN# we use the BMIQ normalised data for the following function
NormBMlist <- readRDS(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/NormBMlist.rds")
## the `CombatFUN`
# MMat=NormBMlist$NormMAll
# phenotype=NormBMlist$phenoDataAll
CombatFUN <- function(MMat, phenotype){
registerDoParallel(cores = 10)
# # df including tissue informations
# Tissue <- c("Placenta", "Amnion", "Chorion", "Decidua",
# "Maternal whole blood", "placental mesenchyme",
# "placental trophoblast", "umbilical cord", "Umbilical cord blood")
# # add all normalised beta values to a list
# for(tissue in Tissue){
# # subset the beta values for one tissue type
# ## one tissue type
# sampleNamesForOneTissue <- phenotype[phenotype$Sample%in%tissue,]
# BetaMat_1Tissue <- BetaMat[,colnames(BetaMat)%in%sampleNamesForOneTissue$Sample_name, drop=FALSE]
#
# ## normalise beta value for this tissue type
# ListToJoin <- list()
# # names for the list
# listElements <- c(paste0("normB", "_", str_replace_all(Tissue, " ", "_"), ".df"))
#
# # fill the list with beta values
# ListToJoin[[listElements]] <- BMIQ(beta = BetaMat_1Tissue) %>%
# as.data.frame() %>% rownames_to_column(var="Probe")
# }
#
# # left_join values form all samples
# Join_allNorm.df <- ListToJoin %>% purrr::reduce(left_join, by = "Probe")
# # omit na values
# Join_allNorm.df_v1 <- na.omit(Join_allNorm.df)
# # as matrix
# Join_allNorm.df_v2 <- Join_allNorm.df_v1 %>% remove_rownames() %>%
# column_to_rownames(var="Probe") %>% as.matrix() # 298179
# phenotype_matched <- phenotype[match(colnames(MMat),
# phenotype$Sample_name),]
#
#
# # add all normalised beta values to a list
#
# for(t in Tissue){
# # subset the beta values for one tissue type
# ## one tissue type
# phenotype_matched_oneTissue <- phenotype_matched[phenotype_matched$Sample%in%t,]
# MMatOneTissue <- MMat[,colnames(MMat)%in%phenotype_matched_oneTissue$Sample_name,drop=FALSE]
#
# ListToJoin <- list()
# # names for the list
# listElements <- c(paste0("CorrectM", "_", str_replace_all(t, " ", "_"), ".df"))
# phenotype_matched_oneTissue$Trimester[phenotype_matched_oneTissue$Trimester%in%NA] <- "unknown"
#
# if(t=="Placenta"){
#
# ListToJoin[[listElements]] <- champ.runCombat(beta = MMatOneTissue,
# pd = phenotype_matched_oneTissue,
# variablename = "Trimester",
# batchname = "Study",
# logitTrans = FALSE) %>%
# as.data.frame() %>% rownames_to_column(var="Probe")}
#
# batch1 <- factor(phenotype_matched_oneTissue$Study)
# modcombat <- model.matrix(~ 1,
# data = phenotype_matched_oneTissue)
#
# # adjust bach effect for preprocessed mval using Combat function
# placenta_Mval_combatAdjusted1 <- ComBat(dat = MMatOneTissue, batch = batch1, mod = modcombat,
# par.prior = TRUE, prior.plots=TRUE)
#
# # }else{
# # # fill the list with combat corrected M values
# # ListToJoin[[listElements]] <- champ.runCombat(beta = MMatOneTissue,
# # pd = phenotype_matched_oneTissue,
# # variablename = "Sample",
# # batchname = "Study",
# # logitTrans = FALSE) %>%
# # as.data.frame() %>% rownames_to_column(var="Probe")
# #
# # }
#
# }
#
# # left_join values form all samples
# Join_allCorrectedM.df <- ListToJoin %>% purrr::reduce(left_join, by = "Probe")
# # omit na values
# Join_allCorrectedM.df_v1 <- na.omit(Join_allCorrectedM.df)
# # as matrix
# Join_allCorrectedM.df_v2 <- Join_allCorrectedM.df_v1 %>% remove_rownames() %>%
# column_to_rownames(var="Probe") %>% as.matrix() # 298179
phenotype_matched <- phenotype[match(colnames(MMat),
phenotype$Sample_name),]
# phenotype_matched$group <- phenotype_matched$Sample
# phenotype_matched$group[phenotype_matched$Sample%in%"Placenta"] <- paste0("Placenta", phenotype_matched$Trimester[phenotype_matched$Sample%in%"Placenta"])
# ## use Combat to correct batch effects between studies
# MMat_batchCorrected <- champ.runCombat(beta = MMat,
# pd = phenotype_matched,
# variablename = "group",
# batchname = "Study",
# logitTrans = FALSE)
## use Combat from csv package
batch1 <- factor(phenotype_matched$Study)
Samples <- factor(phenotype_matched$Sample)
trimester <- factor(phenotype_matched$Trimester)
Outlier <- factor(ifelse(phenotype_matched$Additional_Info%in%"Outlier", "Outlier", "Standard"))
modcombat <- model.matrix(~ Samples+trimester+Outlier)
MMat_batchCorrected <- ComBat(dat = MMat[,colnames(MMat)%in%phenotype_matched$Sample_name],
batch = batch1, mod = modcombat, par.prior = TRUE, prior.plots=FALSE)
# return list containing beta and M values
## calculate Beta values
BetaMat_batchCorrected <- 2^MMat_batchCorrected / (1+2^MMat_batchCorrected)
# return beta and M values
BM_List_combat <- list(Beta=BetaMat_batchCorrected,
M=MMat_batchCorrected,
PhenoData=phenotype_matched)
return(BM_List_combat)
}
CombatFUN to correct batch# MDSnormCali551_M modified BMIQ calibrated data
BMall_combat <- CombatFUN(MMat = NormBMlist$NormMAll,
phenotype = NormBMlist$phenoDataAll)
## Found15batches
## Adjusting for12covariate(s) or covariate level(s)
## Standardizing Data across genes
## Fitting L/S model and finding priors
## Finding parametric adjustments
## Adjusting the Data
#plotMDS plots
## phenodata for these samples
## check names are in the same order
table(colnames(BMall_combat$Beta)==BMall_combat$PhenoData$Sample_name)
##
## TRUE
## 551
## plot MDS plot
par(mfrow=c(1,1))
MDS_normCorrect551.Beta <- plotMDS(BMall_combat$Beta, top=nrow(BMall_combat$Beta),
labels= BMall_combat$PhenoData$Sample, gene.selection="common")
par(mfrow=c(1,1))
MDS_normCorrect551.M <- plotMDS(BMall_combat$M, top=nrow(BMall_combat$M),
labels= BMall_combat$PhenoData$Sample, gene.selection="common")
AllMMDSinfo <- ggplotMDS(MDS_norm551 = MDS_normCorrect551.M,
GEO_phenotypes_norm551 = BMall_combat$PhenoData,
value = "correctedMv1")
save(BMall_combat, MDS_normCorrect551.Beta, MDS_normCorrect551.M,
file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/GEO_joinedSamples_NormBatchCorrect551_BetaM_MDS_OutlierConsidered.RData")
Mplacenta_combat <- BMall_combat$M[,BMall_combat$PhenoData$Sample%in%"Placenta"]
lebels <- BMall_combat$PhenoData[BMall_combat$PhenoData$Sample%in%"Placenta",]
plotMDS(Mplacenta_combat, top=nrow(Mplacenta_combat), labels = lebels$Sample, gene.selection = "common")
ggplotMDS function again# for MDS_normCorrect551_Beta
AllBetaMDSinfo <- ggplotMDS(MDS_norm551 = MDS_normCorrect551.Beta,
GEO_phenotypes_norm551 = BMall_combat$PhenoData,
value = "correctedBeta")
AllBetaMDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(AllBetaMDSinfo$Study))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# for MDS_normCorrect551_M
AllMMDSinfo <- ggplotMDS(MDS_norm551 = MDS_normCorrect551.M,
GEO_phenotypes_norm551 = BMall_combat$PhenoData,
value = "correctedM")
AllMMDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(AllMMDSinfo$Study))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
NormBMlist list: batch not corrected# MDS_norm551.M or NormBMlist$MDS_norm551.M
table(rownames(NormBMlist$MDS_norm551.M$distance.matrix)==NormBMlist$phenoDataAll$Sample_name)
##
## TRUE
## 551
MDSinfo_uncorrected <- ggplotMDS(MDS_norm551 = NormBMlist$MDS_norm551.M,
GEO_phenotypes_norm551 = NormBMlist$phenoDataAll,
value = "unBatchCorrectedM")
MDSinfo_uncorrected %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_uncorrected$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# MDS_norm551.Beta or NormBMlist$MDS_norm551.Beta
table(rownames(NormBMlist$MDS_norm551.Beta$distance.matrix)==NormBMlist$phenoDataAll$Sample_name)
##
## TRUE
## 551
MDSinfo_uncorrected_beta <- ggplotMDS(MDS_norm551 = NormBMlist$MDS_norm551.Beta,
GEO_phenotypes_norm551 = NormBMlist$phenoDataAll,
value = "unBatchCorrectedBeta")
MDSinfo_uncorrected_beta %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_uncorrected_beta$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# save plots
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/allSamplesMDS551_notCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfo_uncorrected %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_uncorrected$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
pdf(file = "/home/qianhui/DNAme/Process_decidual/figures/allSamplesMDS551_notCorrected.pdf",
width = 13, height = 7)
theme_set(theme_bw())
MDSinfo_uncorrected %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_uncorrected$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
quantro to look at global differences between tissue types (all 551 samples)qtest <- quantro(object = NormBMlist$NormBAll[,NormBMlist$phenoDataAll$Sample%in%c("Placenta","Amnion")],
groupFactor = NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Sample%in%c("Placenta","Amnion"), ]$Sample)
## [quantro] Average medians of the distributions are
## not equal across groups.
## [quantro] Calculating the quantro test statistic.
## [quantro] No permutation testing performed.
## Use B > 0 for permutation testing.
qtest
## quantro: Test for global differences in distributions
## nGroups: 2
## nTotSamples: 495
## nSamplesinGroups: 10 485
## anovaPval: 0.02096
## quantroStat: 40.07735
## quantroPvalPerm: Use B > 0 for permutation testing.
# check difference between outliers and other placenta samples
pd_placenta <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Sample%in%c("Placenta"), ]
Outlier <- factor(ifelse(pd_placenta$Additional_Info%in%"Outlier", "Outlier", "Standard"))
qtest_outlier <- quantro(object = NormBMlist$NormBAll[,NormBMlist$phenoDataAll$Sample%in%"Placenta"],
groupFactor = Outlier)
## [quantro] Average medians of the distributions are
## not equal across groups.
## [quantro] Calculating the quantro test statistic.
## [quantro] No permutation testing performed.
## Use B > 0 for permutation testing.
qtest_outlier
## quantro: Test for global differences in distributions
## nGroups: 2
## nTotSamples: 485
## nSamplesinGroups: 9 476
## anovaPval: 0
## quantroStat: 45.9536
## quantroPvalPerm: Use B > 0 for permutation testing.
anova(qtest_outlier)
## Analysis of Variance Table
##
## Response: objectMedians
## Df Sum Sq Mean Sq F value Pr(>F)
## groupFactor 1 0.09849 0.09849 46.685 2.52e-11 ***
## Residuals 483 1.01898 0.00211
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Note: we can see from the quantroStat value (40.0351) from qtest that difference between tissue types were larger than difference within groups.
# check sample (551 samples) order first
table(colnames(NormBMlist$NormBAll)==NormBMlist$phenoDataAll$Sample_name)
##
## TRUE
## 551
table(colnames(NormBMlist$NormMAll)==NormBMlist$phenoDataAll$Sample_name)
##
## TRUE
## 551
# subset 1st and term samples
Sample_1st <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Trimester%in%"First",]
Sample_term <- NormBMlist$phenoDataAll[NormBMlist$phenoDataAll$Trimester%in%"Term",]
# subset 1st and term Beta values
NormBAll_1st <- NormBMlist$NormBAll[, colnames(NormBMlist$NormBAll)%in%Sample_1st$Sample_name]
NormBAll_Term <- NormBMlist$NormBAll[, colnames(NormBMlist$NormBAll)%in%Sample_term$Sample_name]
# subset 1st and term M values
NormMAll_1st <- NormBMlist$NormMAll[, colnames(NormBMlist$NormMAll)%in%Sample_1st$Sample_name]
NormMAll_Term <- NormBMlist$NormMAll[, colnames(NormBMlist$NormMAll)%in%Sample_term$Sample_name]
# plot MDS for 1st and term separatly
## 1st trimester Beta
MDS_NormBAll_1st <- plotMDS(NormBAll_1st, top=nrow(NormBAll_1st),
labels = Sample_1st$Sample,
gene.selection = "common")
MDSinfo_NormBAll_1st <- ggplotMDS(MDS_norm551 = MDS_NormBAll_1st,
GEO_phenotypes_norm551 = Sample_1st,
value = "MDS_B_T1_samples")
### use MDS info. and plot with ggplot
MDSinfo_NormBAll_1st %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_shape_manual(values=1:length(MDSinfo_NormBAll_1st$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
## Term Beta
MDS_NormBAll_term <- plotMDS(NormBAll_Term, top=nrow(NormBAll_Term),
labels = Sample_term$Sample,
gene.selection = "common")
MDSinfo_NormBAll_term <- ggplotMDS(MDS_norm551 = MDS_NormBAll_term,
GEO_phenotypes_norm551 = Sample_term,
value = "MDS_B_term_samples")
### use MDS info. and plot with ggplot
MDSinfo_NormBAll_term %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_shape_manual(values=1:length(MDSinfo_NormBAll_term$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
## 1st trimester M
MDS_NormMAll_1st <- plotMDS(NormMAll_1st, top=nrow(NormMAll_1st),
labels = Sample_1st$Sample,
gene.selection = "common")
MDSinfo_NormMAll_1st <- ggplotMDS(MDS_norm551 = MDS_NormMAll_1st,
GEO_phenotypes_norm551 = Sample_1st,
value = "MDS_M_T1_samples")
### use MDS info. and plot with ggplot
MDSinfo_NormMAll_1st %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_shape_manual(values=1:length(MDSinfo_NormMAll_1st$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
## Term M
MDS_NormMAll_term <- plotMDS(NormMAll_Term, top=nrow(NormMAll_Term),
labels = Sample_term$Sample,
gene.selection = "common")
MDSinfo_NormMAll_term <- ggplotMDS(MDS_norm551 = MDS_NormMAll_term,
GEO_phenotypes_norm551 = Sample_term,
value = "MDS_M_term_samples")
### use MDS info. and plot with ggplot
MDSinfo_NormMAll_term %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_shape_manual(values=1:length(MDSinfo_NormMAll_term$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
Note: we can’t use combat to correct for batch (for the 1st and term samples), because at least one covariate is confounded with batch! So we need to use sva to regress out batches.
# CombatFun2
CombatFUN2 <- function(MMat, phenotype, trimester){
registerDoParallel(cores = 10)
phenotype_matched <- phenotype[match(colnames(MMat), phenotype$Sample_name),]
phenotype_matched$Outlier <- factor(ifelse(phenotype_matched$Additional_Info%in%"Outlier", "Outlier", "Standard"))
if(trimester=="First"){
TissueTypes <- c("Placenta", "Decidua",
"placental mesenchyme", "Maternal whole blood",
"placental trophoblast")}
if(trimester=="Term"){
TissueTypes <- c("Placenta", "Amnion", "Chorion", "Decidua", "Umbilical cord blood")
}
ListToJoin <- list()
for(i in TissueTypes){
# subset MMat
MMat_i <- MMat[, phenotype_matched$Sample%in%i, drop=FALSE]
# subset phenotype_matched
phenotype_matched_i <- phenotype_matched[phenotype_matched$Sample%in%i, , drop=FALSE]
# use combat to correct batches
if(ncol(MMat_i)>1 & length(unique(phenotype_matched_i$Study))>1){
if(length(unique(phenotype_matched_i$Outlier))>1){
batch <- factor(phenotype_matched_i$Study)
Outlier <- factor(phenotype_matched_i$Outlier)
modcombat <- model.matrix(~Outlier, data = phenotype_matched_i)
MMat_batchCorrected_i <- ComBat(dat = MMat_i,
batch = batch, mod = modcombat, par.prior = TRUE, prior.plots=FALSE)
}else{
batch <- factor(phenotype_matched_i$Study)
modcombat <- model.matrix(~1, data = phenotype_matched_i)
MMat_batchCorrected_i <- ComBat(dat = MMat_i,
batch = batch, mod = modcombat, par.prior = TRUE, prior.plots=FALSE)
}
}else{
MMat_batchCorrected_i <- MMat_i
} # end if
ListToJoin[[i]] <- MMat_batchCorrected_i %>% as.data.frame() %>% rownames_to_column(var="Probe")
} # end for
# left_join values, to join all samples
Join_allM_NormCombat.df <- ListToJoin %>% purrr::reduce(left_join, by = "Probe")
# omit na values
Join_allM_NormCombat.df_v1 <- na.omit(Join_allM_NormCombat.df)
# as matrix
Join_allM_NormCombat.df_v2 <- Join_allM_NormCombat.df_v1 %>% remove_rownames() %>%
column_to_rownames(var="Probe") %>% as.matrix()
# return list containing beta and M values
## calculate Beta values
BetaMat_batchCorrected <- 2^Join_allM_NormCombat.df_v2 / (1+2^Join_allM_NormCombat.df_v2)
# return beta and M values
phenotype_matched2 <- phenotype[match(colnames(BetaMat_batchCorrected), phenotype$Sample_name),]
Combat_BM_List <- list(Beta = BetaMat_batchCorrected,
M = Join_allM_NormCombat.df_v2,
PhenoData=phenotype_matched2)
return(Combat_BM_List)
}
# # Combat correct for batch, use `CombatFUN2`
BM_T1_combat <- CombatFUN2(MMat = NormMAll_1st,
phenotype = Sample_1st,
trimester = "First")
## Found3batches
## Adjusting for1covariate(s) or covariate level(s)
## Standardizing Data across genes
## Fitting L/S model and finding priors
## Finding parametric adjustments
## Adjusting the Data
BM_Term_combat <- CombatFUN2(MMat = NormMAll_Term,
phenotype = Sample_term,
trimester = "Term")
## Found8batches
## Adjusting for1covariate(s) or covariate level(s)
## Standardizing Data across genes
## Fitting L/S model and finding priors
## Finding parametric adjustments
## Adjusting the Data
save(BM_T1_combat, BM_Term_combat, file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/BM_T1Term_CombatCorrected.rds")
# plot MDS for Combat ajusted data: T1 and term
# plot combat Correct_T1_M
MDS_T1_combat <- plotMDS(BM_T1_combat$M, top=nrow(BM_T1_combat$M),
labels = BM_T1_combat$PhenoData$Sample, gene.selection = "common")
MDSinfoT1_combat <- ggplotMDS(MDS_norm551 = MDS_T1_combat,
GEO_phenotypes_norm551 = Sample_1st,
value = "T1_M_CombatremoveBatchEffect")
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/T1SamplesMDS_CombatCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfoT1_combat %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfoT1_combat$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
# plot Combat Correct_Term_M
Outlier <- factor(ifelse(BM_Term_combat$PhenoData$Additional_Info%in%"Outlier", "Outlier", "Standard"))
MDS_Term_combat <- plotMDS(BM_Term_combat$M, top=nrow(BM_Term_combat$M),
labels = Outlier, gene.selection = "common")
MDSinfoTerm_combat <- ggplotMDS(MDS_norm551 = MDS_Term_combat,
GEO_phenotypes_norm551 = BM_Term_combat$PhenoData,
value = "Term_M_removeBatchEffect")
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/TermSamplesMDS_CombatCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfoTerm_combat %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_color_manual(values = "#00BFC4")+
scale_shape_manual(values=1:length(MDSinfoTerm_combat$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
# use sva to regress out batches
svaFUN <- function(SamplePheno, NormM){
# factors to consider
Sample <- as.factor(SamplePheno$Sample)
Trimester <- as.factor(SamplePheno$Trimester)
batch <- factor(SamplePheno$Study)
# M values
mval <- NormM
# factor that interested
mod <- model.matrix(~Sample, data = SamplePheno)
# adjustment variables
mod0 <- model.matrix(~1, data = SamplePheno)
sva_M <- sva(mval, mod, mod0)
summary(aov(sva_M$sv ~ batch)) %>% print()
# use removeBetachEffect
design = model.matrix( ~ Sample, data= SamplePheno)
y <- removeBatchEffect(mval,
# batch = NormBMlist$phenoDataAll$Study,
# batch2 = NormBMlist$phenoDataAll$ArrayType,
# covariates = NormBMlist$phenoDataAl$ControlPC1,
covariates = sva_M$sv[,1:3],
design=design)
return(list(sva_M=sva_M, mval_sv1Removed=y))
}
svaCorrect_T1_M <- svaFUN(SamplePheno = Sample_1st, NormM = NormMAll_1st)
## Number of significant surrogate variables is: 5
## Iteration (out of 5 ):1 2 3 4 5 Response 1 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 4 0.65579 0.163948 20.957 9.963e-10 ***
## Residuals 44 0.34421 0.007823
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 2 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 4 0.4409 0.110224 8.6743 2.98e-05 ***
## Residuals 44 0.5591 0.012707
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 3 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 4 0.49511 0.123777 10.787 3.512e-06 ***
## Residuals 44 0.50489 0.011475
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 4 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 4 0.21199 0.052997 2.9592 0.02998 *
## Residuals 44 0.78801 0.017909
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 5 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 4 0.04291 0.010728 0.4932 0.7407
## Residuals 44 0.95709 0.021752
svaCorrect_Term_M <- svaFUN(SamplePheno = Sample_term, NormM = NormMAll_Term)
## Number of significant surrogate variables is: 27
## Iteration (out of 5 ):1 2 3 4 5 Response 1 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.31886 0.039857 20.422 < 2.2e-16 ***
## Residuals 349 0.68114 0.001952
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 2 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.4182 0.052274 31.357 < 2.2e-16 ***
## Residuals 349 0.5818 0.001667
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 3 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.18612 0.023265 9.9763 1.574e-12 ***
## Residuals 349 0.81388 0.002332
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 4 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.4245 0.053063 32.179 < 2.2e-16 ***
## Residuals 349 0.5755 0.001649
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 5 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.30361 0.037951 19.019 < 2.2e-16 ***
## Residuals 349 0.69639 0.001995
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 6 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.18041 0.0225515 9.6029 4.869e-12 ***
## Residuals 349 0.81959 0.0023484
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 7 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.3219 0.040237 20.709 < 2.2e-16 ***
## Residuals 349 0.6781 0.001943
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 8 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.24282 0.0303526 13.99 < 2.2e-16 ***
## Residuals 349 0.75718 0.0021696
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 9 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.39314 0.049143 28.262 < 2.2e-16 ***
## Residuals 349 0.60686 0.001739
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 10 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.29021 0.036277 17.837 < 2.2e-16 ***
## Residuals 349 0.70979 0.002034
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 11 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.49283 0.061604 42.391 < 2.2e-16 ***
## Residuals 349 0.50717 0.001453
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 12 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.22697 0.028371 12.809 3.513e-16 ***
## Residuals 349 0.77303 0.002215
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 13 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.17758 0.0221978 9.4199 8.485e-12 ***
## Residuals 349 0.82242 0.0023565
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 14 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.06875 0.0085937 3.2206 0.001513 **
## Residuals 349 0.93125 0.0026683
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 15 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.05812 0.0072653 2.692 0.006947 **
## Residuals 349 0.94188 0.0026988
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 16 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.02952 0.0036899 1.3269 0.2287
## Residuals 349 0.97048 0.0027807
##
## Response 17 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.10967 0.0137082 5.3734 2.192e-06 ***
## Residuals 349 0.89033 0.0025511
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 18 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.07176 0.0089704 3.3727 0.0009664 ***
## Residuals 349 0.92824 0.0026597
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 19 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.02194 0.0027427 0.9787 0.4523
## Residuals 349 0.97806 0.0028025
##
## Response 20 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.03489 0.0043616 1.5772 0.1302
## Residuals 349 0.96511 0.0027654
##
## Response 21 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.01888 0.0023597 0.8394 0.5684
## Residuals 349 0.98112 0.0028112
##
## Response 22 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.03457 0.0043208 1.5619 0.135
## Residuals 349 0.96543 0.0027663
##
## Response 23 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.0169 0.0021120 0.7498 0.6474
## Residuals 349 0.9831 0.0028169
##
## Response 24 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.11464 0.0143297 5.6486 9.357e-07 ***
## Residuals 349 0.88536 0.0025369
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 25 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.0424 0.0053001 1.9316 0.05446 .
## Residuals 349 0.9576 0.0027438
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 26 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.01788 0.0022349 0.7942 0.6081
## Residuals 349 0.98212 0.0028141
##
## Response 27 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 8 0.04331 0.0054142 1.9751 0.04871 *
## Residuals 349 0.95669 0.0027412
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
save(svaCorrect_T1_M, svaCorrect_Term_M, file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/svaCorrect_T1Term_M_CombatCorrected.rds")
# plot svaCorrect_T1_M
MDS_T1 <- plotMDS(svaCorrect_T1_M$mval_sv1Removed, top=nrow(svaCorrect_T1_M$mval_sv1Removed),
labels = Sample_1st$Sample, gene.selection = "common")
MDSinfoT1 <- ggplotMDS(MDS_norm551 = MDS_T1,
GEO_phenotypes_norm551 = Sample_1st,
value = "T1_M_removeBatchEffect")
MDSinfoT1 %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfoT1$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# plot svaCorrect_Term_M
MDS_Term <- plotMDS(svaCorrect_Term_M$mval_sv1Removed, top=nrow(svaCorrect_Term_M$mval_sv1Removed),
labels = Sample_term$Sample, gene.selection = "common")
MDSinfoTerm <- ggplotMDS(MDS_norm551 = MDS_Term,
GEO_phenotypes_norm551 = Sample_term,
value = "Term_M_removeBatchEffect")
MDSinfoTerm %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfoTerm$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
# load the data of control probes
# Control551_Beta, Control551_M
load(file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/Controls_BM_all551.RData")
## Response MDS$x varies with control PC1:
table(NormBMlist$phenoDataAll$Sample_name==rownames(Control551_M$PCA_control$ind$coord))
##
## TRUE
## 551
table(colnames(NormBMlist$NormMAll)==rownames(Control551_M$PCA_control$ind$coord))
##
## TRUE
## 551
cor.test(NormBMlist$MDS_norm551.M$x, Control551_M$PCA_control$ind$coord[,1])
##
## Pearson's product-moment correlation
##
## data: NormBMlist$MDS_norm551.M$x and Control551_M$PCA_control$ind$coord[, 1]
## t = -3.8686, df = 549, p-value = 0.0001226
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## -0.24312317 -0.08046545
## sample estimates:
## cor
## -0.162901
## Fit model:
NormBMlist$phenoDataAll$ControlPC1 <- Control551_M$PCA_control$ind$coord[,1]
NormBMlist$phenoDataAll$ControlPC2 <- Control551_M$PCA_control$ind$coord[,2]
# NormBMlist$phenoDataAll$ControlPC3 <- Control551_M$PCA_control$ind$coord[,3]
design1 <- model.matrix(~ControlPC1+ControlPC2, data= NormBMlist$phenoDataAll) #ControlPC1+ControlPC2
## fit lm using limma:
fit1_limma <- lmFit(NormBMlist$NormMAll, design = design1)
fit2_limma_eBayesAdjusted <- eBayes(fit1_limma)
Residuals <- residuals.MArrayLM(fit2_limma_eBayesAdjusted, NormBMlist$NormMAll)
MDS_residuals <- plotMDS(Residuals, top=nrow(Residuals),
labels = NormBMlist$phenoDataAll$Sample, gene.selection = "common")
MDSinfo_residuals <- ggplotMDS(MDS_norm551 = MDS_residuals,
GEO_phenotypes_norm551 = NormBMlist$phenoDataAll,
value = "MDS_residuals")
save(Residuals, file = "/home/qianhui/DNAme/Process_decidual/RDSfiles/allSamplesResiduals_ControlCorrected_residuals.rds")
## plot MDS with ggplot
MDSinfo_residuals %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_residuals$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
## use `removeBatchEffect`
Sample <- as.factor(NormBMlist$phenoDataAll$Sample)
Trimester <- as.factor(NormBMlist$phenoDataAll$Trimester)
design = model.matrix( ~ Sample+Trimester, data= NormBMlist$phenoDataAll)
y <- removeBatchEffect(NormBMlist$NormMAll,
# batch = NormBMlist$phenoDataAll$Study,
# batch2 = NormBMlist$phenoDataAll$ArrayType,
# covariates = NormBMlist$phenoDataAl$ControlPC1,
covariates = Control551_M$PCA_control$ind$coord[,1:2],
design=design)
MDS<- plotMDS(y, top=nrow(y), labels = NormBMlist$phenoDataAll$Sample, gene.selection = "common")
MDSinfo <- ggplotMDS(MDS_norm551 = MDS,
GEO_phenotypes_norm551 = NormBMlist$phenoDataAll,
value = "M_removeBatchEffect")
MDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
## Now residuals are not correlated with age:
# cor.test(lm1$residuals, dat$age)
## Residuals vs original
# plot(lm1$residuals, dat$y)
## ... Now use lm1$residuals instead of dat$y
# save plots
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/allSamplesMDS551_controlProbeCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfo_residuals %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_residuals$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
pdf(file = "/home/qianhui/DNAme/Process_decidual/figures/allSamplesMDS551_controlProbeCorrected.pdf",
width = 13, height = 7)
theme_set(theme_bw())
MDSinfo_residuals %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_residuals$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
# 1st trimester & term samples
MDSinfo_residuals_First <- MDSinfo_residuals[MDSinfo_residuals$Trimester%in%"First",]
MDSinfo_residuals_Term <- MDSinfo_residuals[MDSinfo_residuals$Trimester%in%"Term",]
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/T1SamplesMDS_controlProbeCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfo_residuals_First %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo_residuals_First$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
tiff(file = "/home/qianhui/DNAme/Process_decidual/figures/TermSamplesMDS_controlProbeCorrected.tiff",
width = 20, height = 12, units = "cm", res = 300)
theme_set(theme_bw())
MDSinfo_residuals_Term %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
scale_color_manual(values = "#00BFC4")+
scale_shape_manual(values=1:length(MDSinfo_residuals_Term$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))
dev.off()
## png
## 2
# factors to consider
Sample <- as.factor(NormBMlist$phenoDataAll$Sample)
Trimester <- as.factor(NormBMlist$phenoDataAll$Trimester)
batch <- factor(NormBMlist$phenoDataAll$Study)
# M values
mval <- NormBMlist$NormMAll
# factor that interested
mod <- model.matrix(~Sample+Trimester, data = NormBMlist$phenoDataAll)
# adjustment variables
mod0 <- model.matrix(~1, data = NormBMlist$phenoDataAll)
sva_M <- sva(mval, mod, mod0)
## Number of significant surrogate variables is: 37
## Iteration (out of 5 ):1 2 3 4 5
summary(aov(sva_M$sv ~ batch))
## Response 1 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.30135 0.0215251 16.514 < 2.2e-16 ***
## Residuals 536 0.69865 0.0013034
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 2 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.07017 0.0050123 2.8894 0.0003129 ***
## Residuals 536 0.92983 0.0017348
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 3 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.17209 0.0122922 7.9581 1.688e-15 ***
## Residuals 536 0.82791 0.0015446
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 4 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.02815 0.0020109 1.1091 0.3463
## Residuals 536 0.97185 0.0018131
##
## Response 5 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.36046 0.0257473 21.579 < 2.2e-16 ***
## Residuals 536 0.63954 0.0011932
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 6 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.08745 0.0062464 3.6689 7.141e-06 ***
## Residuals 536 0.91255 0.0017025
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 7 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.09013 0.0064380 3.7926 3.855e-06 ***
## Residuals 536 0.90987 0.0016975
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 8 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05338 0.0038126 2.1588 0.008317 **
## Residuals 536 0.94662 0.0017661
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 9 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.1958 0.0139858 9.3216 < 2.2e-16 ***
## Residuals 536 0.8042 0.0015004
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 10 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.16031 0.0114508 7.3094 4.914e-14 ***
## Residuals 536 0.83969 0.0015666
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 11 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.1356 0.0096855 6.0058 4.399e-11 ***
## Residuals 536 0.8644 0.0016127
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 12 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05087 0.0036336 2.052 0.013 *
## Residuals 536 0.94913 0.0017708
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 13 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.1256 0.0089713 5.4993 6.146e-10 ***
## Residuals 536 0.8744 0.0016313
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 14 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.08038 0.0057411 3.3462 3.5e-05 ***
## Residuals 536 0.91962 0.0017157
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 15 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.11982 0.0085585 5.2118 2.734e-09 ***
## Residuals 536 0.88018 0.0016421
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 16 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.13163 0.0094021 5.8034 1.263e-10 ***
## Residuals 536 0.86837 0.0016201
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 17 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.0699 0.0049930 2.8774 0.000331 ***
## Residuals 536 0.9301 0.0017353
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 18 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.07199 0.0051425 2.9702 0.0002136 ***
## Residuals 536 0.92801 0.0017314
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 19 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.07846 0.0056041 3.2595 5.335e-05 ***
## Residuals 536 0.92154 0.0017193
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 20 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05513 0.0039381 2.234 0.006036 **
## Residuals 536 0.94487 0.0017628
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 21 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05323 0.0038023 2.1526 0.008535 **
## Residuals 536 0.94677 0.0017664
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 22 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.08955 0.0063964 3.7657 4.409e-06 ***
## Residuals 536 0.91045 0.0016986
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 23 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.10239 0.0073134 4.3671 2.114e-07 ***
## Residuals 536 0.89761 0.0016746
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 24 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.11336 0.0080973 4.8951 1.407e-08 ***
## Residuals 536 0.88664 0.0016542
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 25 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.03902 0.0027869 1.5545 0.0879 .
## Residuals 536 0.96098 0.0017929
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 26 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05842 0.0041730 2.3755 0.003262 **
## Residuals 536 0.94158 0.0017567
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 27 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.0849 0.0060642 3.5519 1.275e-05 ***
## Residuals 536 0.9151 0.0017073
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 28 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.09111 0.0065081 3.8381 3.07e-06 ***
## Residuals 536 0.90889 0.0016957
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 29 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.01975 0.0014108 0.7714 0.7008
## Residuals 536 0.98025 0.0018288
##
## Response 30 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.02179 0.0015563 0.8528 0.6112
## Residuals 536 0.97821 0.0018250
##
## Response 31 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.02555 0.0018248 1.0037 0.4478
## Residuals 536 0.97445 0.0018180
##
## Response 32 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05687 0.0040618 2.3084 0.004376 **
## Residuals 536 0.94313 0.0017596
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 33 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.04436 0.0031686 1.7772 0.03882 *
## Residuals 536 0.95564 0.0017829
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 34 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.08067 0.0057624 3.3597 3.277e-05 ***
## Residuals 536 0.91933 0.0017152
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 35 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.03595 0.0025675 1.4275 0.1353
## Residuals 536 0.96405 0.0017986
##
## Response 36 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.06901 0.0049292 2.8379 0.0003983 ***
## Residuals 536 0.93099 0.0017369
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Response 37 :
## Df Sum Sq Mean Sq F value Pr(>F)
## batch 14 0.05076 0.0036261 2.0475 0.01324 *
## Residuals 536 0.94924 0.0017710
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# use removeBetachEffect
design = model.matrix( ~ Sample+Trimester, data= NormBMlist$phenoDataAll)
y <- removeBatchEffect(NormBMlist$NormMAll,
# batch = NormBMlist$phenoDataAll$Study,
# batch2 = NormBMlist$phenoDataAll$ArrayType,
# covariates = NormBMlist$phenoDataAl$ControlPC1,
covariates = sva_M$sv[,1],
design=design)
MDS<- plotMDS(y, top=nrow(y), labels = NormBMlist$phenoDataAll$Sample, gene.selection = "common")
MDSinfo <- ggplotMDS(MDS_norm551 = MDS,
GEO_phenotypes_norm551 = NormBMlist$phenoDataAll,
value = "M_removeBatchEffect")
MDSinfo %>%
ggplot(aes(x, y)) +
geom_point(aes(shape = Tissue, col=Trimester), alpha = 1, size = 5)+
# scale_color_manual(values = namedPal2)+
scale_shape_manual(values=1:length(MDSinfo$Tissue))+
labs(x="Dimension 1", y="Dimension 2")+
theme(text = element_text(size=15))